today is Wednesday September 11th this is lecture four and we are continuing with chapter four microbial cell structure and function for your attendance the access code is 8858 word of the day is UK carote remember spelling counts it doesn't matter if the first letter is capital or lowercase please pay attention before you hit send you have two chances remember to look up once you're done so I can see when everyone's finished give you about 30 seconds and remember usually around this time in the semester after we've gotten a couple weeks in there's more questions if something is really burning you and it does not make sense it's okay to raise your hand chances are if you're struggling like that there's 50 other people that are struggling in the same way with that same thought so you'd be helping the whole class by answering your question to those of you that sit right here I try to take a good look but sometimes this computer blocks My Views so if you're trying to get my attention and I don't see you just kind of wave your arm a little bit all right write it down if um you weren't able to submit it so you still have the info but I'm going to move on today is an important day September 11th uh 2001 that's when the World Trade Centers were hit I feel older and older every year because I believe you all weren't even born when this happened right exactly so I remember exactly where I was uh when this happened I was in school school um was in grade school I won't tell you what grade and uh just the whole world whole country shut down um because of this many people lost their lives I actually have a good friend of mine that was a survivor of this and my father was a veteran he was not a part of this but he was a veteran so anybody military family even if you weren't born were all affected by this so I just wanted to take a quick moment of silence for 911 okay your homework reminder um remember the extra credit was already finished if you did not submit assignment one please do that as soon as possible um there's a couple of you that were listening I really appreciate that if you submit any homework assignment late after the due date please send me a message on canvas so that I can manually check your grade and make sure it's what it's supposed to be um sometimes there's zeros there just depends on when I sync it and if you completed did it late you do get some credit so please let me know if you submitted anything late so that I can update that grade we do have assignment two that will be due this Friday by 5:00 pm we're going to get into a routine such that most Fridays you'll have a homework assignment due remember all of them are accessible on Pearson's and canvas if you want to get ahead you can so just um showing you the remainder of our unit one schedule I updated this just for this slide we're going to finish chapter 4 today and then we're going to move on to chapter 5 next week afterwards we'll have one class for chapter 6 and seven you'll see that's more of um a shorter um chapter we really only have chapter six there's a small part of chapter seven very small so it's not really two chapters in the same way like chapter four and chapter five is big and then on that Wednesday we will have a review session and the exam will become available that day as well we went over this last class just make sure that you download the lockdown browser I can send an announcement to everyone to the whole class but you know you do have access to this on canvas and uh these slides where you can see the link all right a quick review on chapter three there's a couple important topics I want to make sure everyone is clear on because chapter 3 is important just for your fundamentals of biology no matter where you go in your career and there's a couple important questions that if you don't understand these Concepts you're going to miss a couple points on your exam all right remember a good way to to gauge um like your progress if you can talk through this with your study group then you're in a good place you'll also see that I posted your study guide with more key terms that's available on canvas so that study guide I actually go through each question on the quiz and I make sure that I put all the major topics on that study guide right so really take advantage of that both your learning objectives that I place and your study guide how many of you have a study group already or a study buddy o not enough people okay let's ask the other question who does not have a study buddy or a study group raise them High look around make friends a lot of times in college you don't have to study with your friends and there's pros and cons to each I'll say sometimes I study with my friends sometimes I study with my classmates you don't have to be friends with someone to study with them and there's a lot to be gained by studying with someone that is different personality wise than you are you might see things differently you might think differently and you can learn from each other so please make sure you have some type of study buddy so that you can get some feedback on where you're at with the material it's very easy to convince yourself that you know it and you're doing well when you're isolated when you talk to someone else then you can really get a feeling of okay I know this or I need to study this a little bit more all right Graham stain is fundamental in biology all of you that are going into the clinic are going to be familiar with graham stain so remember the purpose of this we have to to classify bacterium into certain groups so that we can understand the functionality and also when we talk about antimicrobial techniques we understand how to defend ourselves against these microbes this is one of the first tests that we developed for biology you can have gram positive which stains purple or gram negative which stains pink someone asked a very wonderful question that I appreciate I want to say this to the whole class just because you see that a lot of rods are pink that does not mean that rods are by definition gram negative you'll see that commonality a lot of times rods are gram negative but it doesn't mean that they have to be so when we're talking about the shapes of bacteria um that are in chapter four remember that's just the shapes this stain right here is regarding you know Grand positive or gram negative and they can be of any shape right so again it's an indication of the cell ball structure gram positives they can be tend to kill by penicillins or detergents the reason for that remember think about like washing your hands with soap that type of detergent because Grand positives do not have that double membrane they're easier for our defenses to attack and Destroy them gram negatives are more resistant to antibiotics they're more durable they have that outer membrane which forms like a shield in many ways and they also have that toxin that's a problem LPS so make sure you all heard me which one has LPS positive or negative positive negative very good all right the Gram stain method make sure you memorize this protocol and don't just memorize the steps I want you to think about if something goes wrong what would it look like so for example if I forgot to apply the iodine the Morant which is like the glue for the crystal Violet what would happen to our results if I forgot to apply the Morant you can shout it out let's think through this okay step one is to apply the crystal Violet very good none of the crystal Violet would stay if we forgot to apply the Morant so if we stopped right there and did not go to or step four the whole slide would look clear or colorless there's a difference between colorless and white so we say colorless in this type of situation right does makes sense to everyone I want you to think like that because you will have a question like that all right let's get to chapter four so we didn't get into chapter four that much on Monday but we will finish it today definitely and maybe we'll have a couple um minutes for questions at the end all right so make sure all of the stuff that I you know colored in red is important make sure you can talk through these things remember the concept is just as important as the definition if you just know the definition without understanding how it plays into the whole you know picture of biology you're not going to get the grade that you want on your exam definitions will only get you halfway there all right so make sure you understand the difference between a procaryote and a eukaryote our procaryotes are more simple cells they're smaller no organel they have circular chromosomes all right and then our ukar are more complex they have paired chromosomes histones which we use to kind of wrap our chromosomes around you'll understand in our next couple chapters why we have histones and they have organel all right so make sure you understand the difference and then we went over our basic shapes I'm not going to spend too much time on this because we did that on Monday but just make sure you understand the difference between our bassilus the rod shaped the caucus the spherical and then the spiral you have the spiralini the vibrio and the spirite so understand the definitions and be able to recognize the pictures if I gave you one of these pictures would you be able to select the right one as far as the name from multiple choice all right and these are aoxy the spirals we have some odd shaped ones like stars and rectangulars I posted this article on canvas if anyone's interested in reading it at your leisure um you can definitely do so sometimes it helps to understand and place everything into perspective but this is optional you don't have have to read it we talked about Pepto glycan that is the major component of the cell walls it provides the mechanical rigidity to the cell and it protects the cytoplasm and determines the cell form and when I say cell form I'm talking about the shape we talked about these nag n repeats that's how the Pepto glycan is formed the backbone and they're linked together through these um peptide cross Bridges all right this is important you will have a picture you'll see either the gram positive or the gram negative and then you'll be asked a question about it you could be asked you know is this gram positive or is it gram negative you could ask you know which one has teic acids which one has LPS so really make sure you bit a big star on this slide that you can recognize it and be able to answer questions to differentiate between the two then we have our bacterial cell walls this is kind of more detailed from the previous slide just again it's showing you in more detail and be able to recognize which is which if you see the picture our gram negative um you know the outer membrane remember they have this um LPS it's composed of lipid a and the O polysaccharide antigen these little blue um circles right here these are like porn protein so it's like a channel think of it like a doorway to allow things in or out all right we went over the structure already and this was the last slide that we truly got to the glyco calic so remember that is the sticky material it's made of polysaccharides that's outside the cell wall so if it's neatly organized then that's going to form a capsule and the capsule is like a shield to the bacterium when bacterium have capsule it's harder for um phagocytosis meaning other immune cells to eat the bacterium to destroy it if it's unorganized and loose it forms a slime layer so this glyco calic is important because it allows cells to attached to surfaces and form biofilms biofilms are like a cluster of different bacterium imagine if each of us were a bacterium and we decided we were going to work together for whatever defense and we all had different personalities and different things we bring to the table but we come together and form some massive like unit that's what's happening in a biofilm a lot of times when patients have implants and they have a bofilm that develops if you can't kill it with antibiotics a lot of times that implant has to be removed because biofilms can really create a nasty infection that is very difficult to treat because they have that like hard slime layer that's protecting it from all of our antimicrobial defenses all right we talked about our fella this is just the types of it you can go back to our last lecture to review this one and this is truly where we left off so remember flagella is like the tail or the legs of the bacterium all right so it's made of chains of felon and it's attached to a protein hook that's anchored to the wall and the membrane by the basil body right so if you're looking at this this is the filament here's the hook basil body body and then this is the plasma membrane right here so remember it's anchored inside the plasma membrane and then it shoots out like a tail all right so the assembly it's built from the inside out and it's Guided by these certain proteins the rod cap the hook cap and the filament cap Rod hook filament you'll never be asked that but still so again Rod hook filament there is a quick little YouTube video which I'm going to show you it's just a couple seconds that shows you the development of fella so remember that's our rod that's being formed inside the cell membrane this is our hook cap that's coming there we go and then the filament is what ends up shooting out all right so it starts from the inside out and you do have the link to see this YouTube video yourself it's just a quick animation all right you can watch the rest on your own it's almost over anyway all right so when we talk about motile cells we're talking about motion all right so how do these cells move that remember the fella is like the legs so we can rotate the flagella to run or tumble all right so if you want to move towards or away from a stimulus that's called taxis so think about you know if you're at the mall and you smell like Cinnabon if you like cinnamon rolls and then you decide hm I want to go over there to buy cinnamon roll that's what taxes is yes yes they can fella can be in procaryotic and eukariotic cells and we're going to go over the difference very good question so this is for our procaryotic cells all right so the fella proteins they're H antigens that's just kind of trivia you don't have to know all of that part but we have this bias random walk so when moving towards a stimulus we run longer and we tumble less if we're moving away from it then we run less and we tumble more all right so it's just kind of like think about if you smell something great Cinnabon your Grandma's favorite cookies whatever and it brings you down to you know that location of where it is and I use that comparison because we're talking about procaryotes but the same concept exists in humans too we are also very dictated by our smells all right when we're talking about axial filaments this is an endoflagella so in spires Endo means inside EXO or Ecto means outside all right make sure you remember those roots again Indo inside Ecto or EXO outside I want you to get into the habit of critically thinking with science you can memorize all day long but we all have our capacity for how much we can remember the way to be good scientist which all of you are in this class is to be able to think critically about what you're seeing all right so inpat they're anchored at one end of a cell and then the rotation causes the cell to move something just happened with our recording on my laptop goodness give me one second guys there we go okay and now we're going to talk about fim and pilli so this is a proteinous fibers protonations means full of protein and they're protruding from the bacteria protruding meaning sticking out so all of these little lines that look like little hay fibers that's the fimbr so the fimbr allow attachment to surface and cells so it's like a bunch of little arms reaching out to give handshakes real quick what does temm stand for shout it out what type of scope you know the EM part what's that electron what about the T transmission very good all right and the pilli so that facilitates transfer of DNA from one cell to another via conjugation you have this glitching and twitching motility the grappling hook of how the pilli kind of attached to one another and some can even conduct electricity think about nanowires right so here's just an example this is the sex pillis between two cells and it's how we're able to get kind of um like reproduction in that binary fision process all right the plasma membrane this is something hopefully we've all seen before but we're going to go into a little bit more detail all right so remember that when we're looking at these different um phospholipids it's kind of like a circle with two legs so the circle at the top is what's polar or hydrophilic meaning it likes to be around water it's attracted to water and we call this circle the head versus these little lines are the Tails right so the head is polar meaning it likes water hydrophilic means it likes water so filic means to like Hydro is water always remember your root words I hope that you're all creating kind of your science dictionary it's going to save you a lot of time throughout your studies from undergrad and beyond all right then we have our non-polar Tails they're hydrophobic and they're composed of fatty acids so we have two phospholipids that kind of join together in this Arrangement one you can consider right side up one is upside down and what ends up happening is this um lipid by layer right here it allows us to keep you know our cytoplasm inside and the periplasm outside it separates and creates a nice divider the way we have things that travel from one side or next to the cell whether it's outside to the inside or inside to the outside we have these pores that are like channels or doors we're going to learn that there's specific um antigens that will allow and sometimes it's not antigen sometimes it's chemical if you have a certain concentration of sodium on one side you know anyone taken Neuroscience before Action potentials kind of similar concept all right so there's just a magic code or key once that formula happens then it's like putting that key into the door for something to pass right let's make sure everyone understand plasma membrane this is important okay and that relates to the fluid mosaic model so the membrane is viscous like olive oil means kind of like sticky that's what viscous means the proteins move to function so even though we see these blue um circles right here that are stationary in reality they're moving back and forth because of this viscous kind of olive oil type um structure of this phospholipid bilayer and the phospholipid they can rotate and move laterally so just because you know this guy is on the top right here it can move side to side it can even decide to jump to the bottom remember the head is what's polar meaning it likes water the tail is what's non-polar hydrophobic all right so here we go this is some terminology you will have questions on these we're talking about movement of materials across the membrane whether it's in to out or out to end how do we figure out how things move across the membrane so the first process we're going to talk about is simple diffusion simple diffusion is defined as movement of a solute from an area of high concentration to an area of low concentration a solute just means some type of substance or chemical within a solution all right and we move with simple diffusion we're going to move down the gradient so think about like um teeter totter you know at the playground I don't know if you guys still have those but or like a balance beam so you want everything to be balanced so if some one side has too much of something or is in high concentration it's going to naturally try to go to the other side so that on the sides of the membranes it's more equal all right so the high gradient at the top meaning higher concentration it's going to move to the lower concentration and these SE little orange dots are solutes they can represent anything this could be sodium this could be glucose could be anything all right and it's going to travel through the membrane all right to the area of lower concentration to balance itself out all right now we have facilitated diffusion which means the solute combines with the transporter protein in the membrane there's no energy source so here's a non-specific transporter right here this little blue Channel and it's allowing these positive ions to go through versus we have a specific transporter and it has a specific shape to allow something specific to go through so this one is specifically from glucose all right so B is showing us a facilitated diffusion through a non-specific transporter so it means that these substances can't go through the membrane they have to go through this channel over here with C this is facilitated diffusion through a specific transport it means that a specific substance needs to find its specific door to enter right make sense so let me put this in real terms I've all been to college before many different colleges I know SDSU still has a party reputation so think about this if you're trying to go to a club and you want to get in VIP you have to have a certain badge or a certain friend with you to get into VIP you can't just roll up same concept make sense yeah anyone confused on this okay so movement of materials across membranes we're going to continue so both simple and facilitated you notice that did not require energy it's something that just happens to balance itself out based on concentration when we're talking about active transport or group translocation that means we need energy to go from one place to the next using my club example imagine if you're trying to get in someplace you need money a cover fee you can't just go inside same thing so active transport it requires a transporter protein and ATP ATP is a type of energy group translocation requires a transporter protein and P another type of energy so remember both require an energy source to transport solutes against a concentration gradient that's why it requires energy so suppose we have something that's low concentration on one side and even though it's low concentration we still want all of it to go to the other side we're going to need energy to move across or against the gradient think about a salmon they they swim upstream salmon are very big and muscular energy is required to go against the current or against the gradient all right osmosis you have question on osmosis osmosis is the movement of water across a selectively permeable membrane from an area of high water to an area of lower water concentration all right we have to keep track of our water balance in our system water is very important if you don't have enough water that's an issue for all of your cellular functions that's why dehydration if not treated can lead to fatality water is that critical for life and not just water the right concentration of water do think about um anyone fish in here anyone go fishing no one fishes okay I fish there's a difference between saltwater and freshwater fish if you take a saltwater fish and put that into a freshwater pond that's going to be a problem the fish is gonna die and I'm gonna explain to you why that happens all right so water can move through the lipid layer or it can be moved through aquaporins or water channels so it means the water can naturally go through the layer or there specialized channels called aquaporin for the water to pass through there's three terminologies I need you to remember again you will be tested on this so an isotonic solution means that the concentration is equal on the outside or the inside so there's no water no net water movement that occurs and keyword net movement water is constantly moving at all times but no net movement means that the concentration stays the same hypotonic solution so water moves into the cell if the cell wall is strong it contains the swelling if the cell wall is weak or damaged the cell bursts this is called osmotic Lis Lis means to burst we're going to talk about Lis in many different um contexts in this class so it's a hypotonic solution we're talking about the solution which means there's a less concentration on the outside so water's going to go in water is going to move wherever it can to make the other side less concentrated it wants to balance out the solutes and the water so because there's more solutes on the inside of this cell water is going to move inside to help dilute that as opposed to a hypertonic solution the water moves out of the cell causing it cytoplas them to shrink all right so there's not enough water that's in the cell so it causes the cytoplasma strink plasmolysis and that's another form of cellular death so my example about putting a saltwater fish into freshwat that fish would basically blow up and if you do the vice versa the other fish would basically shrink and shrivel up if you put a freshwater fish into a saltwater pond it's going to dehydrate and triple up quickly all right so really think about this example so that you can understand what's happening with water and osmosis be able to Define these terms isotonic hypotonic hypertonic if you were given an example you know of one of these pictures and you're supposed to answer which way does water move be able to answer that all right inclusions you do have some type of question about this it's more so matching um and understanding the definitions so we have storage or waste products in all of our bodies in all of our systems every organisms so we have these metachromatic granules they are our phosphate reserves there's many reasons that we need phosphate for example our ATP adenosine triphosphate phosphate carries a lot of energy so we have to make sure we have stores of phosphate we have our polysaccharide granules those are energy Reserves we have our lipid inclusions another type of energy reserve and then we have our sulfur granules which are waste products for human beings we don't have as much need for sulfur as other organisms do and a lot of times sulfur is a byproduct of waste all right think about boiled eggs or any of our bodily functions that smell like boiled eggs sulfur is waste all right I give you guys different analogies all I care about is if you remember right then we have our carboxysomes that's ribulose 15 diphosphate carboxy for carbon dioxide fixation so you don't have to remember that long terminology but remember it's for CO2 fixation there's many different reasons um that we would want CO2 fixation oh and this is another definition thing especially if you don't um speak English as your first language so when we say to fix within biology I'm not talking about something that's damaged and then you're going to repair it different meaning fix means more so to take something in and transform it all right we also have gas vacul that are important for buoyancy there's some cells that need to float and then we have magnetosomes which is iron oxide they sense a magnetic field iron is very important for you know our blood and many different reasons in the body for our functionality so understanding these you know elements and why we need it it matters but you have certain you know inclusions that will sense iron oxide all right endospores we talked about this uh a little bit at the end of chapter 3 because we do have an endospore um you know staining test as opposed to gram staining so an endospore is a resting cell there are some situations in which a cell will rest as opposed to being active and those cells are resistant to desiccation which means dryness heat and chemicals our bassilus or Clum which are Grand positive bacteria form endospores the term sporulation is the process of endospore formation germination is when you would return to the vegetative state or meaning the active state so suppose you in a harsh environment and that bacterium needs to survive a harsh environment there are some you know organisms like our clostridium for example that's able to sporulate meaning to transform itself into Spore version so that it can just have the minimum that is needed to get through that environment and when the environment is safe or better hospitable then it can germinate and return to its active form where it's reproducing and able to exhibit all of its functions this is important some diseases like botulism tetanus or Anthrax in the environment sporulation is one of the reasons that certain bacterium stick around because let's talk about botulism for example or tetanus if you get infected with that and you start trying to give yourself antibiotics or something to kill it those um particular bacterium are able to form spores or go into you know endospore formation as a way to try to stick around a little bit longer and hide all right did I see a hand go up no okay all right this is a nice uh table because it just organizes everything to compare and contrast I highlighted this or put a star on it just because it's a good study sheet A lot of these things you're going to have to understand the difference we will have a specific um time to discuss the ribosomes right here but just remember the 70s is for procaryotes we have the larger ads within ukar all right and let's talk about our UK carots so remember it's more complex than our procaryotic cells and both procaryotes and ukar can have fella as indicated remember our eukariotic cells have organel and this is kind of a hybrid cell because it's showing us plant cells at the top and our animal cells at the bottom we as humans are animals and plants are plants the difference between the organel um our plant cells have chloroplast for respiration and energy production as opposed to animal cells that have mitochondria for energy production when we get into the metabolism chapter mitochondria is the site of the electron transport chain all right so here's a difference you will need to understand the difference between fella for our procaryotes versus our eukariotic cells all right so our UK carotic fella and cyia there's microtubules they're made of tubulin remember our procaryotic cells their fella is made of felin these microtubules are made of tubulin for eukariotic cells we have this nine pairs plus two array so for example here's are our microtubules and these are the nine Pairs and then the plus two in the middle that's what this means all right these are just some um different photographs looking on the outside so this sem means what what typ of scope I heard one person louter scanning electron microscope very good all right so remember this is remember this internal structure of the flagellum or the celium it's showing the 9 plus two array right here this is what it means and only the UK carots have this structure our organel you will have some type of matching question on this hopefully this is review so the nucleus contains the chromosomes the endoplasmic reticulum or ER is your transport Network you can think of that like your freeway the Gogi complex the membrane formation and secretion the lome is a digestive enzymes the vacu it brings food into cells and it provides support the mitochondrian is the site of cellular respiration remember the electron transport chain that's where we're producing ATP our chloroplast for plants the site of photosynthesis again that's the way plants are able to take the sunlight and then transform that into energy that's what photosynthesis means we're going to go over all of that in metabolism then we have our peroxisome which is for oxidation of fatty acids it destroys hydrogen peroxide and croome consists of protein fibers and centrioles remember that's our structure of the cell right so hopefully that's review you do have to understand these definitions uh flash cards are a good way to study this and when I was teaching High School I even did like a whole superhero complex so whatever analogy you have to use in order to remember the functionality of the cells you can definitely do that for the kids like for mitochondria I made a superhero that was like M Mighty mitochondria so that they understood this was like the the strength part where we're getting most of the um the heavy duty like um electron transport chain and respiration so whatever you have to do to remember it all right talking about the nucleus so it's double membranes it's gated by nuclear pores and we have ribosomal RNA that's made in the nucleolus the MRNA or messenger RNA is transported to the cytoplasm and then the DNA genome is bound by histones so these histones are important because they're like little circles and the chromosomes are wrapped around it it's a way of protecting our DNA from damage because remember our DNA that we're born with that has to last us until you know death so we want to make sure that our DNA is not getting degraded such that it would cause um fatality or disease within the organism so histones are one means of protecting your DNA and our mRNA that's messenger RNA when we talk more about you know protein synthesis we'll go over DNA goes to RNA to proteins but that messenger RNA is what contains the actual message or the specific genes that are going to be translated into proteins hopefully that's reviewed then we have our rough OTAs reticulum and the ribosomes so you have the rough ER or the smooth ER the rough ER has bound ribosomes it synthesizes the integral membrane proteins and Export proteins versus the smooth ER has no bound ribosomes and our enzymes make various lipid based compounds like fats and hormones so they have different functions the mitochondrian it houses respiration enzymes it contains its own DNA and ribosomes and the inner membrane system forms christe these little like circular things right here it's so that you can create more surface area to have more room for the electron transport chain so that you can generate as much as much energy as possible and again this is the site of most ATP synthesis for a cell then we have our chloroplast they're double membraned light harvesting structures and it contains its own ribosomes and DNA and the chlorophyll is contained in thids so it's like if you have this large you know piece right here and then the small little circles right here are the phids so a bunch of thids come together to form the chloroplast remember that's in Plants only then our GGI complex it targets membranes and proteins in the Cell It's the side of protein modification such as glycosilation and directional transport Cy or trans sides all right so again this is the site of um targets membrane proteins protein modifications there's many reasons we would modify a protein you'll understand when we talk about protein synthesis that you can somehow take you know one Central thing and then make many different things from it all right and the model of origin of UK carot so I have a star right here because this is critical remember when we were talking about horizontal Gene transfer so this is more a visual of that so the evidence of is showing us that our specific chloroplast and mitochondria they originated as bacterium and then over time evolutionarily these different bacterium ate one another and then um the internal bacterium became our organel we know that because they have their own DNA that can be traced back to early bacterium and then we still have some bacterial species that are of you know the original form so for example chloroplast came from the our cyano bacterium mitochondria came from our proteo bacteria all right so this is our last slide I believe yes it is and so I want to spend the last five minutes or so on questions