hi everyone dr hinky here uh with a video lecture on chapter three our chapter on the cell um so i i'm not gonna do a video lecture for chapter one i think that was some interesting overview information uh that i think you probably all found very helpful um but i think that was pretty easy to read through we're going to go into more in depth on some of the important points uh later on in the semester that really was just an introduction um but the cell here we're going to introduce some information that is probably going to be new to a lot of you chapter 3 has a lot of information it's assumed that the whole second part of the chapter eukaryotic cells you're quite familiar with either from 101 or from an anp class i am going to do a second video that does a quick review of eukaryotic cells and then goes into the specific eukaryotes of microbes that are covered in chapter 5. i'll post that second video this weekend so we're going to go over the first part of chapter 3 on prokaryotic cells there's a lot of interesting information in here and of course the cell structures are going to come up again and again uh so the chapter starts with some history of the cells and discovery of cells our objectives in this first section are to explain the theory of spontaneous generation and then to explain the role of louis pasteur in disproving spontaneous generation we've looked at some of the historic figures i'm very excited to read the enthusiasm that you're showing for learning some of this history it is really fascinating when you think about trying to study microbes and bacteria pre-microscope and pre-tools that we have now to look at these organisms on a molecular level um so it's pretty ingenious and as the discussion has shown a lot of times this was uh these were more accidental discoveries or just someone's passion that they pursued they were persistent in finding an answer they had a question they wanted to know not necessarily that they were just these brilliant geniuses but they were persistent so i think that's one thing we see over and over again in science is that persistence really pays off uh so we'll take a little closer look at some of these historic figures that loom larger than life in our textbooks but really we're just living people so pre uh pre louis pasteur um people believed in spontaneous generation so if you think about this in the before the microscope before we could see on a microscopic level what you could observe what you could see was that hey there was nothing living here and now there's something living here frogs just suddenly appeared in water where there hadn't been frogs before and maggots showed up on meat that was left behind or unspoiled food from nothing uh these you know mice would show up in the barn in a pile of rags where did they come from well they came from cells or they came from mama mouse who had baby mice um but if this wasn't actually observed if you didn't see mom having baby mice and mom usually kept those pretty hidden until they just showed up in their in your barn maggots just showed up on your meat because those fly eggs were invisible so from an observational standpoint it looked like life just spontaneously arose in these places and so one of the first experiments that showed no no maybe maybe we need something else in this picture was uh francesco reddy's meat jar demonstration where he put some mar some meat in an open jar and lo and behold ah maggots the flies were lying in and flying in and out and laid their eggs but when he sealed the jar we didn't have any maggots well nothing got in there and if we covered the jar and cheese we'd find maggots on the top of the cheesecloth because the flies were attracted to that smell they knew there was a food source there and they would lay their eggs there it would be on top but not on the meat so that suggested that life living things living organisms were coming from other living organisms but we still needed conclusive proof and there were different experiments going on really the conclusive absolute definitive we disproved spontaneous generation um and developed the theory of biogenesis so genesis is the creation bio of life uh that living things come from all other living from other living things so louis pasteur uh did this very elegant experiment a lot of these were quite when we look at them now we say oh it's brilliant and the reason they're brilliant is because they're really not complex they're very simple makes them elegant these simple experiments uh where he filled a swan neck bottle so the swan neck flasks this looks like a swan's neck um he put broth in that and this would prevent bacterial and fungal spores from entering and they could get to here and then they'd sort of get trapped down in this bottom part of the of the swan's neck here have liquid it would prevent things from coming in so he boiled and sterilized that broth and when it was cool it remained free of contamination but if we broke off if we took off that neck the part that was preventing anything from coming in then it would get contaminated it would get cloudy this is something you look for in lab if you're working with nutrient broths as cloudiness and that cloudiness are all the bacteria that are growing in there uh so this is a a great quote life is a germ and a germ is life it's a living thing never will the doctrine of spontaneous generation recover from the mortal blow of this simple experiment uh so that disproved spontaneous generation that became a part of modern cell theory is that all cells arise from other cells uh so we're gonna briefly look at the development of that cell theory and how that has evolved well we tend to learn in textbooks at this level that the cell theory has three basic statements to it there are really about 72 so if you think back to the scientific method a theory is a predictive model that has been supported by extensive experimental testing numerous related hypotheses are tested and the more evidence we gather supporting those hypotheses the more we try to disprove them and we can't the stronger our foundation comes at some point we get enough information we get a clear enough picture that we can build a model that can be a predictive model that we can say if i go out and look for this in the real world here's what i'm going to see and then we go into the real world and we see if we can find support or some way to disprove or discredit the theory and the more we try and can't the stronger it is so we'll look how our cell theory these three statements that just remember they're really 72 statements or more than more than that quite a few to give us a complete picture because we know a lot about cells look at how those sort of support everything and how they have evolved up to close to present day with the endosymbiotic theory which is still being expanded we're still testing components of this we're still proposing hypotheses and uh and gathering evidence on this and then we'll look at a few more people who have some incredible contributions to our cell theory and germ theory and things that we'll be studying so cell theory the idea of a cell robert hook back in the late 1600s i think about this about civil war time uh was the first one to describe cells and he looked through a microscope at cork so cork is the bark of the of oak tree quercus uh and this is what it looks like and to him what he what that reminded of him of is in monasteries where the monks are in cells they're all in rows i think like a prison cell very similar all nice neatly road same sized squares and plant cells tend to be larger than many animal cells and very regular in their shape and structure and so that's what that reminded him of and so he coined the term cell um oh not 1865 i said civil war what date was i looking at here dyslexia 200 years before the civil war we got the term cell so some other contributors to this early idea of cells being the foundation of living organisms mattias schleiden was a botanist uh who observed that all plants are made of cells looked under the microscope and saw this same same structure everywhere he looked theodore schwann was a physiologist who saw that animal cells have a lot of similarities to plant cells so animal cells don't have a cell wall so they don't have that always the same repeating structure and very similar rectangular shape that plant cells do but he did see like there were a lot of similarities between these cells uh in the 1800s so now now we're up to uh close to civil war time so just to put that into some historical context of what we knew when uh so as before turn of the century before world war one uh robert rimac died in 1865 but mid-1800s they proposed this extension of abiogenesis as part of the cell theory all cells arise from cells uh so initially what past jurors had proposed is that living things come from other living things this takes this down to a smaller level to the single cellular level how did we get to become a multi-cellular organism with 35 trillion cells just by cells reproducing and making more cells that's through mitosis you remember that from bio 101 and from there continued to expand the modern cell theory to say that all cells only come from other cells so we aren't going to get a cell from anything other than another cell and cells are the fundamental units of all organisms usually a third uh third statement that goes with this it says the cell is the basic unit of life and that really goes hand in hand with cells of the fundamental unit of organisms because a cell by itself a single cell can be a living organism but we are not 35 trillion living organisms we're one living organism made of 35 trillion eukaryotic cells so those two sort of go hand in hand to account for both multicellular organisms and single celled organisms if we removed any one of our cells yes it would still be living it could carry on all the functions of life but only for an indefinite amount of time we couldn't keep that alive indefinitely because it's part of a multicellular structure it needs its related cells whereas a single celled organism can perform all the functions of life by itself so that's why we usually have those two statements together it's just to clarify that point so in 150 years since then continued to study cells continued to learn more about them as new tools and new methods became available to study them as we've been able to look more and more closely we have more powerful microscopes now we have molecular mechanisms that let us look even more closely at cells to continue to refine and develop and add to this theory there are still questions we don't know where did the first cell come from there are a few competing hypotheses about this and if you're interested you can look those up if you'd like to to see what's what's being proposed and the evidence there's evidence uh for um for the various hypotheses that are out there um so the primordial soup tends to probably have the most evidence uh its main competitor is um i can't remember what the name of it is it's basically that the first cell came from outer space which leads to the question where did that cell come from so it doesn't really answer the question only the first cell on earth um i want to say spermatogenesis pam spermia that's what the name of that one is all right so anyway where we've evolved now we have learned quite a bit about cells and both bacterial and eukaryotic cells like our own one of the big questions about cells was how did we how did we get to these big complex cells in eukaryotes um from this single cell the original cells on the planet that our simple life form everything started with a single cell how did we get this great diversity how did we get from that to these more large to these larger more complex cells and then to multicellular organisms in the 1970s let's get started a little bit earlier than that but a researcher named lynn margulis um so maybe in the 60s it was before the 70s and the 60s lynn margulis proposed the endosymbiotic theory uh and what she looked at was looking closely at the components of eukaryotic cell she said huh look at that in animals the mitochondria look an awful lot like bacteria and they're about the same size as many bacteria and then looking at plant cells she said hey look at that the chloroplasts look a lot like bacteria and are about the same size as bacteria the function of mitochondria is to produce energy well living organisms acquire materials use them to get energy and use that energy to build structures uh plants use the energy from sun the chloroplasts use energy from sun to build food and there are prokaryotes that are photosynthetic that look an awful lot like chloroplasts uh lynne was pretty much dismissed at the time because she was a female working in biology in the you know 50s 60s 70s she's got a nice little pat on the head and was dismissed but she persisted and as technology caught up with her and she was able to look more and more closely it turns out that the chloroplast and the mitochondria have a double membrane which is exactly what would happen if one cell ingested another cell you would end up with an outer membrane and an inner membrane that outer membrane being part of the endocytosis process packaging that cell that we just ingested inside a little membrane-bound transport vesicle uh and then so that was some evidence that oh that's how those could have gotten in there uh then we got better and better technology and she was able to extract ribosomes and analyze them and lo and behold eukaryotic ribosomes are structurally different the ribosomes found in animal cells and plant cells are structurally different than the ribosomes that are found in prokaryotes the mitochondria and and the chloroplasts have ribosomes but they're not eukaryotic ribosomes even these even though these are organelles found in eukaryotes they're prokaryotic ribosomes and then she was actually able to extract dna and it turns out that mitochondria and chloroplasts have their very own dna suggesting they were their own individuals now some of the things that have contributed and expanded our understanding of this we found come through those mitochondrial dna when we are born in the original egg cell and sperm cell that come together the mitochondria are found in the egg the sperm only contributes dna so our first mitochondria comes from our mother so our first mitochondria is identical to our mothers subsequent mitochondria come from that first mitochondria dividing and lo and behold the mitochondria divide separate and apart from the rest of the cell but we look at that dna and the dna in our mitochondria is identical to that in our mother's mitochondria doesn't matter if you're male or female our mitochondria came from our mother and hers came from her mother uh and so we can track ancestry back through mitochondrial dna very very very accurately because that mitochondria the only change over time is just this background mutation level so mitochondrial dna tracking that through the maternal lines and eukaryotes where it would come through the maternal egg uh has given us even more evidence that lynn margulis was on to something with the endosymbiotic theory and at the time it was a hypothesis uh now there is more than sufficient evidence that it is accepted throughout um the scientific world throughout biology and sort of that process was there was an original prokaryotic cell that engulfed an external cell an aerobic one in the case of mitochondria a photosynthetic one for the chloroplasts rather than digesting it for food something happened some glitch we'll look at that as we go through the term and it didn't digest it but instead it kept it inside and found hey look at that this mitochondria or this bacteria is pumping out this energy that i can use uh what a good benefit so whatever that glitch was was genetic passed it on to its offspring who also engulfed and failed to digest some bacteria that produced energy for it and on and on over millions of generations until mitochondria became first a symbiont with the cell that engulfed it and then eventually a a complete part of it so mitochondria is no longer a separate free living organism i can't extract my mitochondria and have it go on they are now intricately bound together as part of the same cell that was over millions of generations but the mitochondria retains its own separate dna when the cell is about to divide the nucleus for the eukaryotic cell sends the signals to the mitochondria and the mitochondria divides so that it can get ready to split and have one mitochondria in each daughter cell they can also divide during the regular life of the cell because some cells need more than one mitochondria if they need lots of energy like muscle cells um and then plant cells similar process going on with photosynthetic cells uh so as i said it this doesn't end our theory we continue to investigate look at new things in the late 80s when margulies said hey i'm looking at prokaryotic or bacterial flagella and boy they look a lot like spirulum which is one of our shapes of bacteria and so she started looking at the structures and seeing if maybe that flagella bacteria that have flagella if maybe that's an endosymbiont if that's a relationship that had evolved over time that's still up for debate all right so that's our cell theory and see science is progressive we continue to study and learn and expand and improve our knowledge so we're still studying cells even though we know a lot about them there's still a lot that we don't know another theory that we'll be interested in is germ theory the germ theory of disease states that disease may result from microbial infection i am not going to play the videos in this but when you go through the powerpoint please do click on click on the links for the videos and watch these videos ignace semolice was an obstetrician and what he noticed his observation was that you know physicians would go you know from room to room in the hospital they would go they would perform an autopsy and then they'd go into an examining to an examining room and examine a patient or go to the delivery room and deliver a child and without washing their hands or without changing their clothes or anything in between and so he proposed hand washing he said gee why don't y'all wash your hands in between uh and kind of like some people today who don't believe in wearing masks or washing hands or social distancing uh people rejected this idea of hand washing but it's ridiculous how is that possibly going to prove prevent disease and after his death lo and behold people started washing their hands her physicians started washing their hands and child bed fever the mortality rate in maternity wards significantly decreased ah he also compared that uh infants born by midwives at home were more likely to survive at this time and midwives were hand-washing were very big on promoting cleanliness during childbirth so now we celebrate him as the first proponent of hand washing as a way to prevent the spread of disease but it didn't happen in his lifetime another one another researcher who contributed to our studies of germ theory and in spread of the disease is jon snow everybody can remember jon snow from game of thrones this is not that jon snow but a british physician in the 1800s who tracked down he mapped cases of cholera as cholera was spreading he mapped where cases were popping up and at this time cholera was thought to be this poor person's disease it tended to happen in crowded cities in uh you know around more more densely packed areas in the slums and so people would say oh that just that just affects poor people as he tracked it though when wealthier people in the suburbs and further from the city started to get sick [Music] then people started to get interested in what could possibly be the cause he tracked this and mapped it and found that he could find where uh sort of how the disease was going to spread by saying there are more cases here fewer cases out here fewer out here as i get further away and if i track back to where the most cases are there's a common water source and that common water source was where people were contracting the the cholera that was the source of the cholera outbreak and so he's really considered the father of epidemiology epidemiology is now everyone is much more familiar with it but similar to forensics in that it is tracking it is trying to track and solve questions about the spread of disease so he's the father of epidemiologist and he did this by mapping where people got sick when louis pasteur we've already talked about uh so disproved spontaneous generation and he also discovered that microbes are responsible for food spoilage they're also responsible for fermentation and based on that he proposed that hey if they can spoil food if they can ferment liquids beverages then they could probably cause some problems in our body they might be responsible for infection so he had proposed that but didn't have any way to demonstrate that and as uh we were introduced to in chapter one robert koch is the one the first person who came around along and gave definitive proof he established a causative relationship not just correlation but causative relationship between a specific microbe and a specific disease and he did this um with an experiment where he would get into this in the book a little bit later but um he had a series of mice that were all infected all had the same disease and he isolated bacteria from them and then he isolated what was the common bacteria in the sick mice that the healthy mice did not have he injected that into healthy mice they all developed the same symptoms same disease and died and then he was able to isolate that same bacteria afterward from those mice so showing definitively that these bacteria present with this disease cause this disease in healthy animals so he was able to identify the causative agent and he looked at a number of different bacteria and diseases so coke's postulates are sort of the four steps that are needed to clearly link this pathogen with this disease and we'll look more closely at those in a chapter coming up joseph lister see listerine uh he is a surgeon that was the first to develop aseptic techniques in medical center at settings aimed at reducing microbes he went beyond just washing hands uh with soap and water between visits to different rooms to actually disinfecting hands and air with carbolic acid this is phenol and phenol is sort of our number one can be very toxic but it's our number one cleanser that we rate all disinfectants against phenol and we'll look when we talk about disinfectants and control of growth we'll look at what phenol is and how it works but joseph lister is the first one who began disinfecting using aseptic technique so this gives us our timeline and if we look sort of here back in 1546 we have our very first proposal of germ theory and yet it took almost 350 years till turn of the century before someone was able to specifically causatively specifically link cause and effect from bacteria and infections so ongoing progressive little by little as we learn more and more we can build on that it's quite an interesting history a lot of things that we take for granted now like gee hand washing gee aseptic technique uh when you're performing surgery those were revolutionary at the time all right so now let's get into our cell specific structure so if we look at classification we have three domains we have the bacteria and the archaea which are single-celled simple organisms with no membrane-bound organelles so our domain is bacteria archaea these are both single cells so they're both uh very similar they were both in the same domain until fairly recently when we got molecular techniques that showed that yes they have similar ribosomes but our ribosomes come in two parts and the archaea ribosome is half similar to bacteria and half similar has a lot of similarities to eukaryotes they also have some different cell wall structures so they are significantly different enough to be separated out it's also been was thought that bacteria can cause disease in humans archaea we don't know they've never been known to cause disease in humans maybe they can for quite a while it was just sort of a given that they don't because we've never seen it but now some researchers are suggesting that yeah maybe they can um and then the eukaryotes is what we're familiar with are bigger complex cells that consist of the kingdom's protista which are single celled organisms and algae which algae fall into that even though we have macroalgae that are very huge like kelp the vast majority of algae are phytoplankton or single-celled organisms and and they don't fall quite into the category of plants they don't have plant-like structures uh the kingdom of fungi and plants and then what we know animals all of these kingdoms have more similar cells they have nuclei and they have membrane-bound organelles their cells are much more similar in structure and function than our bacteria which are different in our archaea so we are going to focus on our bacteria just quick review if we look at cells the different types of cells all cells the characteristics that all cells have whether they're prokaryote eukaryote plant animal fungus bacteria archaea they all have dna they all have rna and they all have proteins a lot of textbooks just say dna because rna comes from dna and proteins come from dna and rna but they do have all of those all cells have those you would never find a cell that doesn't have these they all have cytoplasm which is the aqueous solution inside the cell in which everything floats and that's where all of our resources all of our the chemicals that we need the ions that we need everything that we take in uh from eating sort of floating around in here to take place in chemical reactions the cell membrane sometimes referred to as the plasma membrane is our outer wrapping and both bacteria and eukaryotes have plasma membranes plants have plasma membranes animals all cells have a plasma membrane this is the structure that separates inside the cell from outside the cell oop that doesn't belong there all cells don't have membrane-bound organelles that's my bad i meant to cut and paste that there and i got it in the wrong place they do not have membrane-bound organelles sorry cross that out right now so that we don't get confused by that and then i'll change the um the slide in the d2l ribosomes they all have ribosomes ribosomes are an organelle they are a small structure with a specific function inside cells the function of ribosomes is that they are the site of protein synthesis all cells have ribosomes they are an organelle but they don't have a membrane around them so that's why we say that membrane bound organelles are only found found in eukaryotes so our prokaryotes if we compare they have all of these things they're very simple they don't have a lot of complexity they're very small they have no membrane-bound organelles all bacterial prokaryotes have a cell wall for the ones that we're interested in for our bacteria they have a cell wall made of peptidoglycan so that's what we're going to focus on is peptidoglycan there are two groups of bacteria that we're not going to talk about that don't have a cell wall but we're really not going to talk about them other than mycoplasmas and l-form bacteria do not have a cell wall they are the weird bizarre exceptions all the bacteria we're interested in have a cell wall with that's made of peptidoglycan and all prokaryotes exist as single-celled organisms there are no multicellular prokaryotes eukaryotes the cells are significantly larger 10 to 100 times larger than prokaryotic cells they all have a nucleus that is a membrane-bound structure that contains the dna they are complex they have compartments these compartments are membrane-bound organelles that's where that membrane bound organelle belongs i found it oh no there it is they have membrane-bound organelles and that's what gives them compartmentalization so they have endoplasmic reticulum these are little separate rooms they have golgi apparatus they have mitochondria they have all these little separate rooms so different functions can take place in different parts of the cell i like to compare these to a one-room schoolhouse versus one of the buildings on trident tech campus one room schoolhouse grading teaching discipline administration paperwork everything lunch phys ed everything takes place in the same room bacteria everything takes place in this same room in eukaryotes i have separate compartments for separate functions so different things are separated so chemical reactions can be isolated and take place at a faster rate there's less interference things have to move around and that just makes for more efficiency and more ability to specialize and that's given eukaryotes a great advantage so we're going to focus on prokaryotic cells our objectives are to explain the distinguishing characteristics of prokaryotes uh to describe common cell morphologies morphologies and arrangements um describe internal and external structures and compare characteristics of our bacterial and our kale cells we've done that really our bacteria archaea differ archaea have some structures that are found uh more similar to eukaryotic cells and they don't cause disease these are sometimes called extremophiles because they're found in extreme environments they can be methane producers they are found in deep sea hydrothermal vents they are found pretty much everywhere we say oh nothing could possibly live in that environment uh in the hyper salinity of the great salt lake nothing oh yeah archaea are found there nothing could be found at the great pressures at the bottom of the sea oh yeah rk are found there so they tend to live in very extreme environments that's that's about all we're going to talk about archaea so onto our bacteria we'll also describe structure and function of the plasma membrane of the cell wall and other external structures found on them so this is our sample prokaryote of course we'll see everything shown on here these are all the different structures that we might find on a prokaryote so this is a typical prokaryote hypothetical meaning you're probably not going to find one that has all of these structures so we're going to look at the different structures this is just an image to show all the possible structures our prokaryote could have and one shape the bacillus shape so this is so that i can run through and talk about all of these different components the plasma membrane the cell wall the capsule the pilots the flagellum the fimbriae cytoplasm ribosome the nucleoid region the inclusions and plasmid those are all things that bacteria could have what all the bacteria that we will talk about have is a plasma membrane because all cells have a plasma membrane outside of that plasma membrane our bacteria will have a cell wall made of peptidoglycan all bacteria will have cytoplasm the liquid matrix the aqueous solution where everything the cell needs sort of floating around and suspended inside here ribosomes the site of protein synthesis all cells have those so all prokaryotes have those the nucleoid region we don't have a membrane membrane surrounding our dna and separating it from everything else that goes on in the cell but wherever the dna is concentrated we tend to call that the we say that's the nucleoid region this is an aqueous solution this could float all over the place it could be anywhere but dna all cells have dna so there it is and all the rest of these structures some bacteria have some don't and that's really how we identify a lot of bacteria which of these structures do they have which ones don't they have and then biochemically what do the what do they do what are they able to eat what are they able to process how can they use different resources so that's how else we can differentiate them but from physical appearance this is what we're looking at so if we look at the structure of all bacteria of our bacterial cell all bacterial cells possess the cell membrane the cytoplasm ribosomes and that chromosome their dna a single circular chromosome believe it or not that hodgepodge messed up thing of string if we spread that all out it would be one single circular chromosome but it's floating in liquid so it gets all tangled up most bacterial cells possess a cell wall they said the exceptions are the mycoplasmas and the l-form bacteria which we're really not going to talk about other than to mention they don't have a cell wall and most bacteria have some sort of surface coating called a glycocalyx but not all [Music] so structures that are found in some prokaryotes include flagella so flagella you should probably familiar with that are used for motility pillai they're sort of a long looks like a flagella it's really a long modified fimbriae and the fimbriae are these thread-like structures that extend from the plasma membrane out through the cell wall that are used for adhesion so these are all external appendages different uses some have an outer membrane so they have the plasma membrane and then the cell wall and then a membrane layer outside of that not all but some plasmids which plasmids are these little extra extra chromosomal bits of dna so here we said this is a single circular dna this is all the dna this is all the information that tells this bacteria how to survive how to function what to do when plasmids are these extra chromosome extra chromosomal bits of dna the bacteria doesn't need it to survive to function but it's just sort of like bonus dna and this is how bacteria exchange uh genetic information they'll take a plasmid and copy it and say hey this gives me some really cool features i'll make a copy and share it with another bacteria so plasmids are just some little extra bonus dna inclusions inclusions are little clumps or clusters of materials of resources things that the bacteria needs that it wants to hold on to and store they're kind of storage units a lot of these are made of proteins but they can be gases they can be other things that they're just little storage units endospores are a specialized structure that some bacteria make that puts them into essentially hibernation a dormant stage and then intracellular membranes this is just a few instances of this not really common so we'll look at each of these more closely first we'll look specifically at our bacteria since our poster child bacteria here is a bacillus just make sure we know not all bacteria are bacilli bacilli or bacillus singular bacilli's plural um are rod shaped they can be very tiny rods it's just that they are longer than they are wide so it's an oval it's not a circle uh sometimes under the microscope it can be hard to tell because they can be very tiny rods cocci or the singular caucus like streptococcus caucus is spherical these are round bacteria we can have helical or curved bacteria and these we have vibrios are comma shaped so we have the vibrio cholera that causes the causative agent of cholera that's the shape of that bacteria we can have spirulum or spirilla in the plural that are spiral they're kind of helical shaped they twist around uh and spirochetes which have more of a distinct curve spirochetes are rigid versus burling which are flexible and these move by axial filaments so their motion is sort of like a corkscrew you could also have arrangements not all bacteria have arrangements arrangement means uh how they line up one to another after they divide sometimes they divide and they just split apart in their individual cells so you'll just look under the microscope and see lots of individual cells some bacteria species tend to stick together after they divide each cell is still functioning if i split them up it's not a big deal they just continue to divide but as they grow they tend to stick together to get larger larger and larger masses and these can be pretty distinct under the microscope so the arrangement that i get if i just have a single i can have a single caucus i can have lots of single caucuses that are unconnected i have some that when they undergo binary fission and split one cell becomes two those two stay together and then as these divide we'll keep splitting up but we'll stay in pairs we use the prefix diplo to define that diplococcus we can also have diplobacilli you might hear that pronounced diplo british and english tend to have a lot of different pronunciations for these so you'll hear both in the videos but we can be diplo two di being two we can divide uh again and end up as fours or tetrads the two we're going to see more than anything with cocci if they stay in clusters they kind of look like clusters of grapes because they're round we call that strepto i mean for sorry staphylo so staphylococcus can be an adjective describing my bacterial arrangement and type so staphyloe it's a cluster of cocci i can also use that term staphylococcus as the genus so i have to know the difference am i talking about the genus staphylococcus in which case it would be written in italics with a capital s or am i talking about this as an adjective describing the shape and arrangement of my cells in case it would not be italicized and it would be lowercase staphylococcus if my cells stay in chains stay close together in big long strips i call it strypto so strepto uh strepto streptococcus are chains of bacteria and i remember that by saying streptostreptobacilli a long strep a long strip of bacillus uh so those are my different arrangements and sarcina are when i get little cubes so four by four all right if i look inside my cell if i go inside look under an electron scanning electron microscope i would see this area that's a little more dense i see this big long squiggle through it i would define this as my nucleoid region they said we're floating around in aqueous solution the cytoplasm so that's not always necessarily right in the middle it can be all clustered up and clumped up on one end it can be spread out could be just about anywhere but wherever i would find it when i'm looking under the microscope that would be the nucleoid region so it's the condensed area of dna that's visible as not a separate entity but i can identify this under the microscope the dna is circular it's double stranded just like our chromosomes except our chromosomes are in threads and i have many of them here i'd just take one of those and circle it around to get my single uh bacterial chromosome and then those plasmids these little extra chromosomal pieces of dna they're small also circular double-stranded dna because that's what dna is is a double-stranded molecule bacteria can copy these separately and pass them on uh and not keen on the word offspring here because they can make a copy and when they undergo binary fission and divide into two cells they can pass that on but more commonly they make copies of that and pass that on to other cells around them so passing genes down from one cell to offspring to subsequent generations is horizontal gene or it's vertical gene transform transfer going vertically down the generations uh but plasma plasmids are often copied and passed to peers in their cohort so i'm going to pass that on to my friends and my same generation through horizontal gene transfer these aren't essential to bacterial growth and metabolism metabolism and oftentimes they code for things that we call virulence factors things that actually uh help the bacteria to survive and many of those things are also the things that cause problems disease and illness in us so antibiotic resistance is often held on plasmids not in the regular chromosome tolerance to toxic metals the production of certain enzymes and toxins can also be directed by that plasmid so you can see hey i have this cool little chromosome here a little bit of a chromosome that makes me resistant to this antibiotic i'm going to make copies of it and share it with all my friends so since we reproduce just through binary fission we make a clone an exact copy of ourselves there's not a lot of genetic diversity other than through mutation so this is one of the way that bacteria have overcome that to diversify is to be able to share beneficial genes let's see these are used in genetic engineering this is uh they're easy to manipulate transfer from to cell to cell get them to carry specific genes and we will talk about that later ribosomes these are the site of protein synthesis so all cells have ribosomes in prokaryotes we have specific subunit of 30s is the size the large subunit is 50s when they come together the total it's actually not cumulative it's overlapped this is refers to a molecular size actually in the complete chromosome together in the two parts we call a 70s chromosome in prokaryotes ribosomes are made out of proteins and rna that type of rna they're made out of is ribosomal rna and we'll learn more about that in the genetics unit um cytoprotein synthesis this is where i'm going to build all my proteins because proteins especially the classic proteins known as enzymes are responsible for all the chemical reactions that take place in cells and metabolism this is some total of chemical reactions in a cell without enzymes we would have no metabolism so we would have no life uh so these are pretty important we're going to spend a lot of time looking at these and how they work so protein synthesis we're going to make especially for bacteria the enzymes that i need to function inclusions are little intracellular storage bodies they vary in size number and what they hold and bacteria can use those to sort of store resources store food when those are depleted in the environment around them they can store sugar they have gas vesicles in aquatic bacteria which are really bubbles to help them float they can store sulfur in little protein-bound packets and phosphate granules so it's a way to package they don't have membrane-bound organelles but this is a way to package and retain materials endospores so some bacteria are capable of capable of producing endospores and what an endospore is is a dormant resting cell so some gram-positive bacteria like clostridium and bacillus have the ability to do this not all cells do but these cells would be normal cells just like we looked at and they would be metabolically active we call that a vegetative cell but if the conditions around them became very adverse very harsh conditions all the food is gone we're in a drought extreme heat pretty much any adverse environmental condition the bacteria is able to form an endospore so it's a protective structure that isolates the bacteria from the surrounding environment it becomes dormant it's no longer metabolically active it's not growing it's not dividing the endospore really just holds on to the dna and a few enzymes and ribosomes it packages just the smallest about of what's needed and goes dormant that process of building that spore is called sporulation when environmental conditions improve foods available water is available that spore will germinate meaning it will return to a vegetative state so here uh in this image we see bacillus anthraxis which is the causative agent uh when we talk about anthrax anthrax poisoning uh it's the spores that we're releasing um but you can see these the bacillus grows as a streptobacillus we see long change of chains of bacilli this entire purple oblong structure would be a cell so here's a vegetative cell every cell would not form a spore all at once in a whole population here's a vegetative cell so it has not yet formed a spore here's a vegetative cell these white uh circles in here these are actually the spore forming this outer parts the spore inside here would be the dna some ribosomes and a few enzymes would be inside that this vegetative cell now this purple part is going to die off it's no longer going to maintain those cellular structures and we'll end up with just this these spores so here we have a spore sporulation is complete on these white circles sporulation is in process where i have this purple cell with a white circle in the middle of it and i still have metabolically active cells here so i can see all three stages in this image if i zoom in on this process here's my regular normal cell it gets to a certain point it undergoes binary fission one cell becomes two and then i grow i get back to full size uh at some point during this life cycle the environmental conditions go south there's no more food or there's a drought or something and so organisms that are that are able to will form a spore and here we see um what we're going to do is we are going to make a copy of my dna we're going to go through this binary fission process but we're going to divide unequally and then we're going to form a spore coat so this is an organic hard coating on the outside protein coat that's going to form around it that's my spore i have my dna i'm just the minimal stuff that i need in here i form that coat and then eventually this cell lyses it falls apart i'm not putting energy in to maintain it so it's going to fall apart and i just have a spore and then when conditions are improved some water is available the spore will become metabolically active start to create structures and will germinate into a bacterial cell and start the process all over again again take a look at those videos so endospores are considered a virulence factor because they are able to withstand all sorts of efforts to destroy the cells and then when conditions uh are ripe again are good for the for growth out they come and so they can be present even after we think we've gotten rid of all the pathogens they're resistant to ordinary cleaning methods and boiling um really the only way to destroy them is with autoclaving so high pressure steam for 20 to 30 minutes it's quite a lengthy time there are several bacterial species that can produce these uh that are pathogens so anthrax used for bioterrorism attacks clostridium tetani which causes tetanus clots clostridium perfringens which causes gangrene clostridium botulinum which causes botulism and clostridium difficile which a few of you have mentioned that in class which is very difficult to kill internal gut infection so oh see so we have lots of different uh spore producing bacteria endospore producing one thing i do want to point out endospores this is the proper name for bacterial structure that is dormant we often abbreviate it and just say bacterial spores just say spore be very careful to double check if you are talking about a bacterial endospore when you see the word spore or a fungal spore fungal spores are reproductive structures so they're always metabolically active bacterial endospores are not metabolically active but because we abbreviate just a spore casually can sometimes confuse them so make sure you're clear on what type of spore we're talking about all right so on to our some more structures the plasma membrane the plasma membrane all cells have this it's set up similarly in all cells it's a phospholipid bilayer with embedded proteins we call that the fluid mosaic model we'll spend some more time on this membrane is selectively permeable and it is what regulates what can go in and out of the cell so you want to watch the video on diffusion i am going to post a video lecture on diffusion osmosis and membrane transport um later in the term this is going to keep coming up this idea of diffusion osmosis membrane transport we're going to look at it again when we talk about cell growth and when we talk about control of growth and you have an activity on this coming up in the next unit so i'll have that lecture posted to help you through the activity but these are very common biological concepts that you should be familiar with and i find students do tend to struggle with those so facilitated diffusion we're still talking about diffusion a passive transport process we just have a doorway in the plasma membrane and osmosis is a special case of diffusion where the only molecule we're talking about is where water is going to move through a selectively permeable membrane so osmosis is is a special case of diffusion what's special about it is we're only talking about the movement of water and we're talking about that movement through a membrane definitely want to watch the videos on diffusion of osmosis that are in here and refresh membrane transport because this is how things get in and out of cells so this is a pretty important process but it should also be familiar to all of you in a 200 level course our cell wall on bacteria we specifically have a cell wall made of peptidoglycan a cell wall this is outside of the membrane it is a rigid structure our membrane that plasma membrane lets things pass in and out of the cell it's biologically active the membrane let's go back here my membrane is embedded with proteins in eukaryotic cells where i have all those internal membrane bound organelles i have separate compartments where all my metabolic reactions all my chemical reactions that make up metabolism can take place in bacteria i just have this one big room so most of the reactions that take place for respiration for fermentation for pretty much all the chemical reactions take place using these membranes some of these membrane proteins and some of these will act as doorways to let molecules pass in and out and some will act as receptor proteins for cell to cell communication a lot of these many of these especially in prokaryotes act as enzymes they catalyze chemical reactions so we definitely want to review the plasma membrane and that function talk about that more as i said later so that membrane is metabolically active it controls what goes in and out our cell wall is not our cell wall is not metabolically active uh it is the difference it's i like to think of it more as a fence around the cell uh it is a scaffolding around the cell it is rigid um and provides the shape for the cell the reason our cells can have those different shapes is because they have this solid wall around them the cell wall determines shape it prevents the cell from bursting due to changes in osmotic pressure so if um if we are in a very low a hypotonic environment outside the cell fresh water through osmosis that water would try flooding into the cell and it would continue to go into the cell and eventually the cell would burst if it was eukaryotic cell like ours an animal cell but bacteria have that cell wall so at some point the water will no longer be able to enter uh it'll the membrane will press against that wall and the pressure will be equal to the pressure trying to enter and that will stop the water coming in so the cell will not lyse it will not burst um similarly if we're in a hypertonic solution like a really salty solution out here the water portion of my cytoplasm would want to leave the cell um for animal cells that cell would shrivel up here the membrane will pull away from the cell wall that water will be able to leave but the cell will still have its external shape because that wall will keep will continue to have its shape we can define two different types of cell walls and bacteria gram-positive cell walls and gram-negative it's going to be our big way to differentiate our first cut in trying to identify a bacteria we're going to look at the shep at the shape of the cell the arrangement of the cells and their gram reaction so here i have cocci circular cells in clusters and they're gram positive so i can describe these as staphylococcus i don't know if that's the genus staphylococcus because i can have the bacterial cells that stain gram positive that are caucus that are round and that grow in clusters like this that are not the genus staphylococcus so micrococcus is one but so i don't know yet based on this but it would be suggestive and i can describe the adjective use the adjective staphylococcus to describe this here i have um bacilli i have to look close you can see these are fairly small bacilli so it's sort of hard to see but these are oblong uh i don't see any definite arrangement so i just see lots i mean there are a lot of them together but they're not in long strips or chains or clusters they're just sort of all over but these stain a different color they stain pink so these are gram negatives you'll talk about the gram staining process in lab so first the basic structure of peptidoglycan which is the primary component of the cell wall it's a macromolecule that's composed of sugar and short peptide fragments so peptides that's the building blocks of proteins so amino acids so these are my sugars i have big long chains of sugars and these are i don't remember the big long name there's the big long name but nag and nam so i have mags alternating with nam nag alternating with nam and big long chains of these and then those are connected by amino acids amino acids are held together with peptide bonds so this is called a peptide proteins are polypeptides big long long chains these are short chains so it's a peptide of the building blocks of proteins amino acids and what i tend to see when i look at these repeating layers lots and lots of layers of naganim is a chain link fence so if i look at gram positives and gram negatives the big difference is going to be in gram negatives i have a single layer of chain-link fence around my cell a gram-positive has multiple it's very very thick so it would be like having five repeating layers of link fence around my yards on a gram-positive cell wall the peptidoglycan is much thicker because i have lots and lots and lots of layers of it whereas in gram-negatives i just have a few one or two layers of that peptidoglycan so gram-positive are structurally simple i just have lots and lots of layers peptidoglycan i have some tychoic acids external to the plasma membrane um you can use these to identify my cell gram-negative cells are much more complex i've got three different layers my uh where am i here my peptidoglycan layer is very thin one or two layers of peptidoglycan so very very thin for both of these here's my cytoplasm so if we look i'm inside let's progress from inside the cell the cytoplasm next comes my plasma membrane and next comes my peptidoglycan the actual cell wall and i have these anchors um that are specific to my peptidoglycan and gram positives here but thick layers of peptidoglycan my gram negative all right yep here i am cytoplasm my plasma membrane and then outside of that plasma membrane i've got my peptidoglycan but only a single layer and then outside of that i have a second outer membrane this is a lipopolysaccharide so polysaccharide it's a sugar with fats attached to it i have porins these are special protein structures through this outer membrane that allow water to pass because otherwise this is a lipid water would be repelled so i need a way for water to get through uh i have specific proteins on the outside that i can use to identify this but lipid a this is my big one lipid a is a component of the gram-negative cell wall that can actually be a toxin so i'm going to talk about this um because the gram-negative cell wall actually has a toxin in it as long as my bacteria is alive that is not toxic to me when i kill that bacteria and it's released then it becomes toxic and then i connect my my membrane to the cell wall through this protein here so that's my those are my comparisons of a gram-positive and a gram-negative cell wall peptidoglycan is the big important one and peptidoglycan is sugar and peptides nag and nam sugars repeating long chains of sugars held together with peptides with short chains of amino acids there are some bacteria that lack a typical cell wall structure that means that it's not going to give me a gram positive or gram-negative stain almost all bacteria i can differentiate gram-positive gram-negative through the staining process and i know something about their cell wall mycobacterium and nocardia have an atypical cell wall structure they really if i looked at them closely they would really have a gram-positive cell wall they have a thick layer of peptidoglycan but outside of that thick layer of peptidoglycan they have an outer layer it's not a membrane but it's a layer of mycolic acids so these are a waxy substance and that wax it works just like wax if i coat something like wax it's productive or it's protective it's going to protect me from a lot of things so it's similar to that outer lipopolysaccharide membrane in that way and that it provides some protection so it's also a virulence factor it gives a high degree of resistance it protects the cell from a lot of chemicals it also protects it from dyes so when i go through the gram staining process this repels the gram stain dyes so i have to use a special staining procedure to identify mycobacterium and nocardia so what you'll do in lab is the acid fast staining procedure because otherwise these would just repel all the stains you wouldn't see them i'll just point out as i said we aren't going to talk about the two types of bacteria that don't have a cell wall but do be careful mycobacterium looks awful similar to mycoplasma mycoplasmas don't have a cell wall at all mycobacterium have a cell wall that's similar to gram-positive but with mycolic acids this waxy outer coating so i just want to mention that because it is in the book about those mycoplasmas and l-form bacteria that don't have a cell wall uh all right uh outside of the cell wall other structures that might be found outside of the cell wall the glycocalyx glycocalyx is a coating of molecules it's a made of a sugary substance so it's kind of sticky that's outside the cell wall it's made of sugars sometimes there are proteins or lipids mixed in with those sugars so typically some kind of glycoprotein we can have two different types of glycocalyces we have a slime layer which is just very loosely organized it's very loosely attached it's easy to wipe off it can predict protect the cell from dehydration or the loss of nutrients so it's just sort of this like outer jelly coating or i can have a capsule which is highly organized and tightly attached to the bacteria so it makes bacterial colonies mucoid slightly mucusy as you can see here this sort of clearing around the bacteria that's repelling the stain we can see the capsule that's that glycoprotein repelling the capsule and it's making them stick together so that capsule lets bacteria stick to each other remember it's a glycoprotein it's a sugar it's a sugary sort of thing so it's sticky so it can help bacteria stick together here's this could be sort of jelly-like this would be more like jello more organized and tightly attached i like to refer to these because y'all know i'm a harry potter freak i like to repair uh pro refer to the glycocalyx as the invisibility cloak this is going to be produced outside the bacteria attached to it if i am an immune system cell looking to get rid of invaders i'm going around checking out cells looking for cells that don't belong when i touch this cell when i reach out say what are you i see jelly i say or jello either one i say oh your food okay and i don't attack you so it makes the bacteria invisible to the immune system cells it also lets these stick together so that i can mass i can get a large mass of cells together um hopefully we're going to come back for glycocalyx the glycocalyx the sticky the capsule or the slime layer let bacteria stick together and so they form biofilms and a biofilm you're probably all familiar with is dental plaque it's bacteria that stick onto your teeth and then more bacteria stick onto those because of the capsule and the more stick onto those uh and if we don't floss we get a nice heavy thick coating based on that um let's see so glycocalyces can be used for attachment bacteria to bacteria or bacteria to other surfaces fimbriae can also be used for attachment these are these little thread like structures extending out past my cell wall or past my capsule if i have one through here they the fimbriae their little thread like fingers you can see that they make a fringe they're small bristle like uh protein fibers and just think if two of these kind of floated by each other those threads would get tangled and so these can be used to entangle these cells to other cells bacteria that colonize that cause respiratory diseases a lot of them have these fimbriae and they get caught up in the cilia in our upper respiratory tract on the cells along the mucous mucous membranes we'll look at that but they can be used for adhesion so i can stick to other cells so these are considered a virulence factor because this lets me stick to cells so if i have fimbriae and i'm going to infect the upper respiratory tract and the person i'm infecting coughs it's not going to get rid of me i'm going to be kind of tangled up in there because of my fimbriae pilos is the singular pillai is the plural is a modified fimbriae it's longer than the fimbriae [Music] and it has a different role than the fimbriae it can be used for attachment uh you'll hear it referred to as a sex pilots often it's used in conjugation i don't like the term mating either because bacteria don't mate mating is when you have a male and a female and each contributes half of the genes bacteria don't do that bacteria will transfer parts of their dna like the plasmid and the pilous is used during this process so here we have the pilus we have a donor cell that has the pilus and it's extended it out to this recipient cell all right so as i said science is progressive and we learn more as we get better tools um so we could see this when i was in school way back a million years ago in the 80s it was thought the pilots worked like a straw that the cell that had one could extend it out attached to the other cell and then shoot that uh that plasmid the copy of the plasmid over here to this other cell turns out now we know it doesn't work that way it works more like a fishing line throws it over here reels that cell in until they're side by side and then passes that plasmid through the membrane through the cell wall through the cell wall through the membrane into the recipient cell only gram negatives have piluses they are the only ones that can undergo conjugation in this manner and we'll look more closely at conjugation when we get to the genetics chapter so this is a really way for bacteria to give the gift of a piece of dna so um again watch the video and all these we're going through fairly quickly we're going to look more closely at all of these as we go uh so that glycocalyx had mentioned the glycocalyx and how cells can stick together and form a biofilm so that happens here's my surface this happens on boat bottoms if any of you are boaters you know you have to scrub the bottom of your boat periodically as i said dental plaques if you are not a diligent housekeeper biofilms will form the bottom of the sink in the bottom of the shower drain on the dog's bowl you have a surface some original bacteria settle the first organisms and then others come by and stick to each other and we keep getting more and more layers which is how dental plaque forms so these thick living layers are called biofilms they make the scum in the toilet or shower they make rocks and streams slippery plaque on our teeth and they can form on things like catheters and breast implants and pacemakers so this is a really big concern in healthcare fields so the slime layer or the capsule my glycocalyx is really the primary structure we associate with these but the fimbry eye which allow cells to stick together can also be involved in that and there we go the inside of the toilet river rocks this is electron micrograph of or a scanning electron micrograph of the lining of a urinary catheter that's been infected with cells through a biofilm so that's a big way for hospital acquired for nosocomial infections is through catheters uh we also have appendages on our bacteria that are used for motility uh the femoral eye have some ability and the pilots have some ability to twitch the pilots especially can move a little bit by you know twitches doesn't work like a flagella it's not a primary means of motility but it can move the bacteria slightly but the primary structure used for motility uh are the flagella and so bacteria flagella work like many propellers if you remember eukaryotic flagella they work like a whip they do a whipping motion back and forth bacteria flagellus spin they rotate like a propeller they're made of three parts the long filament a hook portion that connects the filament to basically to the anchor which is called the basal body that's the anchor that's the part that goes through the cell wall into the membrane to attach there's slightly different attachments in a gram-negative versus a gram-positive bacteria but both have those three structures bacteria can have different types of flagellar elaine arrangements i can have no flagella atrigus i can be monotricus which is mono single flagella at one end amphitricus if you think ambidextrous i have one at both ends lofo tricus is that i have a bunch at one end and then perry tricus you think um perimeter all the way around the outside the bacteria can use these for motion they use them for chemotaxis so they guide bacteria in the direction in response to external stimulus so chemotaxis i can navigate toward or away from a chemical i can navigate toward her away from light phototaxis and bacteria can change direction so depending on which way their uh flagella is spinning clockwise or counterclockwise they will change direction so if they're rotating their flagella counter lock clockwise they tend to swim straight ahead in a straight line and that's called running if they want to change direction they'll rotate the flagella clockwise and it will cause them to tumble and that allows them to change directions all right so that covers all of the basic structures found in bacterial cells a little bit of history of bacteria i know this says study the structures eukaryotic cells on your own this is foundational this should definitely be review so i'm not going to go through this uh entire rest of the portion of the powerpoints you can do that i will give you a brief summary overview and tell a little story in the next video about how all of our different endomembrane structures work together the nucleus the endoplasmic reticulum the golgi apparatus the transport vesicles uh and the outer membrane so uh we'll go through that watch the videos review this but i'll do a very brief overview of that before we talk more about the um the eukaryotes of interest to microbiology so those are the fungus and the protists my single celled parasites and my helmets my multicellular parasites so we'll talk about that in the next video great thank you