Study guide Ch.1-2 & 5
Study guide Ch.1-2 & 5 BIOL 2500-08
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This 19 page Study Guide was uploaded by Claire Bostic on Saturday September 10, 2016. The Study Guide belongs to BIOL 2500-08 at University of North Georgia taught by Swapna T Bhat in Fall 2016. Since its upload, it has received 24 views. For similar materials see Microbiology for Allied Health Professions in Biology at University of North Georgia.
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Microbiology: The human experience Chapter 1- Microbes Shape Our History Highlight=Key terms Highlight=Important Person Highlight=Important concept What is a microbe? Microbes are tiny organisms that cannot be seen with our unaided eye. We need a microscope in order to see microbes. Thanks to Robert Hooke, a man who built the first microscope, we can see and study them today. Microbes have evolved into multicellular plants and animals, EVEN humans. The oxygen we all breathe is generated BECAUSE of microbes. The type of microbe that produces oxygen in order for us to breathe is called Cyanobacteria. The primary producers in the food web are microbes, because they are everywhere. But not all microorganisms are good, especially for humans. There are some harmful microbes that you would call pathogens. These microbes are like the main ingredient for diseases. TYPES OF MICROBES Prokaryotes VS Eurkaryotes NO NUCLEUS: bacteria & archaea HAVE A NUCLEUS: protozoa & algae - Bacteria: located in all habitats of the biosphere and even underground. - Archaea: type of prokaryote that evolved from bacteria & eukaryotes very very long ago. Some types of archaea are methanogens, which means they releases methane through their metabolism. - Protozoa: single-celled microbes that are motile heterotrophs meaning, eating organic foods. - Algae: These microbes contain chloroplasts that allow them to conduct photosynthesis. Algae are who create the essential base of our food web to an extent. - Viruses: Viruses fall under neither prokaryote nor eukaryote. The reason being is because, they are not an organism. They are noncellular microbes that hold genetic material such as DNA and RNA. The structure of viruses can range from being simple to very complex. Microbes Shape Human History Microbes have been around since before the 17 century. Humans depended on microbes (we still do) and didn’t even know it. Microbes are in the air we th breathe, water we drink, and food we eat. Obviously one day in the 17 century, humans discovered the microbial world (the good and the bad) we lived in and it changed everything. Catherine of Siena (1347-1380) A bubonic plague came through the Italian city of Siena and left a sickening ill that started to kill lots of people. Catherine was someone who served God through helping the sick, so she stayed after the plague and took care of ill and leprosy victims. Robert Hooke (1635-1703) He was the first microscopist to design a systematic way to study the newly discovered world, microbes. Hooke made the 1 compound microscope that held 2 or more lenses to intensify the stgnification. The word “cells” came from Hooke. Robert Hooke was the 1 to observe units of living material so, he called it cells. Antonie Van Leeuwenhoek (1632-1723) Leeuwenhoek became the first person to study single-cell microbes. The way he observed them was through lens he made himself by grinding stronger lenses together. Lazzaro Spallanzani (1729-1799) He was an Italian priest that conducted an experiment in order to disprove the spontaneous generation theory but failed. He put meat both in a flask and boiled it. Microbes began to appear in pairs, and Spallanzani did not understand why yet. Louis Pasteur (1822-1895) Pasteur was a chemist who worked on fermentation on alcoholic drinks. Fermentation is a process where microbes gain energy from converting sugar to alcohol. Furthering his work in fermentation, he then figured out the key proponents of spontaneous generation. It is a theory that microbes come from anywhere spontaneously without any parental organisms. Pasteur did an experiment called, the sawn-necked flask. It is similar to Spallanzani’s attempt to disprove this theory except Pasteur decided to curve the middle part of his flask. Pasteur knew that not all microbes require oxygen to grow, which is why he curved the flask. Results: the flask was free of microbes but then when Pasteur tilted the flask in order for oxygen to get inside and microbes quickly appeared. His experiment helped prove the spontaneous generation theory. John Tyndall (1820-1893) The spontaneous generation theory was tested again by Tyndall, an Irish scientist. He conducted the SAME experiment as Pasteur but got the opposite results. In Tyndall’s results, the meat broth helped create microbes even if it was sterilized. A type of organic material became contaminated with a form of bacteria called, endospores. After proving the spontaneous theory, Tyndall then figured out how to get rid of endospores. You would have to kill the bacteria by boiling it under pressure to generate a higher temperature to get at atmospheric pressure. Autoclave, is the name of the stream pressure device used to sterilize materials. Medical Microbiology & Immunology th In the 18 century, the germ theory of disease was developed. It was a germ theory on how certain diseases arise from specific kinds of microbes. Florence Nightingale (1820-1910) She was a British nurse and statistician who founded the science of medical statistics. After that she went to a war hospital hoping to improve soldiers’ conditions. But the death rate continued to increase and so she created a polar area chart of mortality. She discovered an infectious disease of pathogens that grew fast- more so in the summer. All of this was due to the army’s hygiene and the type of hospitals it allowed. Koch’s Postulates 1.Microbes are seen in cases of diseases but not in healthy people. 2.The diseased host isolates the microbe and it starts to grow in pure culture. 3.When a microbe is put into a healthy host, the same disease still occurs. 4.The strain of microbe shows the same characteristics as obtaining it from a newly diseased host EVEN IF cultured. It stays the same strain. Immunization Prevents Disease The founder of immunology is Edward Jenner. He studied small pox that was spreading around and tried to figure out how to prevent it. Until a milkmaid interested him because she could not get small pox. Since she already had cow pox (a less intense disease than small pox); she was immune from getting small pox. Therefore, Jenner started injecting people with cow pox to see if the outcome would have them protected from small pox. His experiment worked, and he created the small pox vaccination thereafter. Alexander Fleming (1881-1955) He discovered the first antibiotic, Penicillin, that inhibits the growth of the bacterial colonies. He left out tons of petri dishes out in his lab and went on vacation for a few days. He came back and found Penicillin mold on the dish and bacteria forming far from it. What was happening on Fleming’s petri dish is called, zone of inhibition, bacteria resisting the antibiotic. So that is how he discovered Penicillin. But later on, Howard Florey and Ernst Chain, purified Penicillin creating it as it is today, a bacteria cell barrier. Discovery of Viruses Since the 19 century, scientists were very curious as to how a contagious disease would be able to pass through a filter that was blocked by microbial cells. A Dutch microbiologist, Martinus Beijerinck, started to study the tobacco mosaic disease. This disease would become mottled and eventually destroy all the crops. He came to the conclusion that the diseased agent passing through the anti-bacteria barrier could not have been a bacterial cell. Later on, this agent was purified by scientist, Wendell Stanley. He ended up crystallizing the tobacco virus and was awarded the 1946 Nobel Prize. Rosalind Franklin (1920-1958) She was a British scientist who discovered DNA through x-ray diffraction crystallography. She used this x-ray to help figure out other kinds of structures present in viruses. Microbes in our Environment Sergei Winogradsky (1856-1953) A Russian scientist to first study microbes in their natural habitats. He walked through the wetlands discovering new forms of microbes that had a metabolism strange to human digestion. Organisms that would feed only on inorganic minerals were called, lithotrophs. When Winogradsky started to observe and study lithotroph organisms, he used an experiment called enrichment culture. When certain classes of the microbial metabolism are supported by the use of selective growth. Later, it was shown that bacteria had a certain role to perform in geochemical cycling- organic and inorganic forms having a global interconversion. The DNA Revolution The Discovery of DNA Rosalind Franklin discovered DNA but was not awarded nor acknowledged for her work. The discovery of DNA come to be because of Maurice Wilkins, Franklin’s colleague. Wilkin’s showed Franklin’s work, without her consent, to Franklin’s opponents, James Watson & Francis Crick. The structured pattern of the double helix of DNA led Watson and Crick to figure out the complementary paring of bases of DNA. Later on, their work was published and Franklin was never acknowledged, at least at that time. Chapter 1 definitions 1. Genome- the whole DNA sequence of every organism. 2. Autoclave- method of sterilizing 3. Germ theory of disease- certain diseases are caused by other kinds of microbes. 4. Cutaneous anthrax is infected by Bacillus anthracis and can be healed by ciprofloxacin 5. Staphylococcus epidermis is a common skin bacterium 6. Bubonic plague was caused by Yersinia pestis 7. Tuberculosis is caused by Mycobacterium tuberculosis 8. AIDs is caused by human immunodeficiency virus (HIV) 9. Chain of infection- transmitting a disease 10. Pure culture- microbe that is grown from a single parental cell. 11. Colonies- isolated bacteria grown from a single cell. 12. Petri dish- a laboratory tool created by Richard J. Petri. 13. Agar- gel substance 14. H. pylori caused stomach ulcers and gastritis 15. Vaccination- smaller and weaken dose of the disease or virus. 16. Immunity- resistant to a disease 17. Antiseptic- kills microbes 18. Aseptic- clean and free of microbes 19. Antibiotic- molecule that kills microbes leaving the host 20. Nitrogen fixation- changing nitrogen into ammonia 21. Endosymbionts- organisms living inside bigger organisms. 22. Mitochondria is similar to respiring bacteria 23. DNA sequencing- reading DNA base paring 24. Syphilis, is caused by Treponema pallidum 25. Ear infection and meningitis is caused by Haemophilus influenza END OF CHAPTER 1 Microbiology: The Human Experience Chapter 2- Basic Concepts of Infectious Disease Highlight=Key Term Highlight=Important concept Highlight=DON’T FORGET Normal Microbiota Vs Pathogens Human beings are 30% human cells & 70% bacteria. We humans are called microbiota to bacteria, archaea, and eukaryotic microbes because we are their home. But, there is mutualism where community members and the host both benefit one another. The normal microbiota has proteins called adhesions where it enables them to attach and colonize the epithelium cells that line our mucous membranes. But it can be kind of tricky to define normal microbiota because, humans harbor organisms that are good and bad (pathogen). Therefore, in order to figure out if the organism is a pathogen, we must observe its pathogenicity. Its pathogenicity is the organism’s ability to cause a disease. We establish this by figuring out the genetic make- up, location on host’s body, and the host’s response (immune system). For example, E. coli is an organism that is bad and good. E coli has two strains: E coli JMD (good guy) & E coli 0157 (bad guy). But even though E coli JMD is most of the time the good cop, IF it happens to get into the urinary tract it will cause a Urinary Tract Infection (UTI). Terminology of Pathogenesis Primary pathogens- microbes that cause diseases to break the walls of a healthy host. An example is Shigella flexneri, which causes bacillary dysentery. Opportunistic pathogens- cause disease in host already sickened or has been breached. A fungus called, Pneumocyctis jirovecii, can easily infect people but it rarely causes a disease. But this type of pathogen can cause life-threatening infections to those who have AIDs because HIV has eroded the immune system. Some microbes are super tricky because, they can enter a latent state during an infection. When they enter this state, they cannot even be found by culture. Virulence- measures “how severe the disease” is and there are two ways to measurement. Letal dose, which is the most commonly one used, measures the number of bacteria needed to kill 50% of the experimental group. The other measurement is Infectious dose, which determines the number of microbes needed to cause disease symptoms in 50% of experimental groups. There are two other aspects of pathogenesis, invasion and invasiveness. The comparison between them is that invasion is when the pathogen invades and then lives inside the host! But invasiveness is when the pathogen spreads through tissue. Fundamental Host-Pathogen Interactions There are five ways that a pathogen can enter our bodies and three ways it can successfully interact with the hosts. Interacting with host 1. Attach themselves on adhesions (type of proteins on the surface of microbes) and/or other receptors and determines their host range 2. Avoiding the immune system by changing their molecular shape to confuse the immune system. Pathogens are so sneaky that they, like Staphylococcus aureus, can secrete molecules to tell the immune system cells that everything is A-Okay! Another interesting thing that pathogens can do that is totally messed up is, telling or convincing immune system cells to basically kill themselves (apoptosis). 3. Lastly, the pathogen has to obtain nutrients from the hosts. The pathogen mainly consumes iron uptakes. The way it does that is by stealing iron from bacteria such as, Siderophore that can bind to iron. Pathogens can even tell the bacteria to get iron from other proteins and bring it back to them. It’s like having minions to do everything for you. Basic Concepts of Disease A disease is when the normal structure of function is disrupted in any parts of the body. But an infectious disease is to be caused by a microorganism that is transferred from one host to another. Signs Vs Symptoms The difference between sign and symptom is that signs can only be observed and symptoms can only be felt by the patient. When signs and symptoms occur at the same time they represent a certain disease, this is called syndrome. Diseases and infections can go away but sometimes they leave behind or cause damage to another organ or part of the body (sequelae). Stages of an Infectious Disease There are five stages of a disease that is like a battle between the infectious agent and a host progress. 1. Incubation pd: This happens right after a microbe initially infects a person through a door of entry. During this period, the microbe’s goal is to replicate more of itself, even by using devices like a thick capsule coat to hide from the host immune system. 2. Prodromal phase: it is very quick and short and kind of unclear. This period is the “warning” phase! It involves symptoms that give you a heads up on the infection or more serve symptoms you are about to get. 3. Illness phase: This is when the usual signs and symptoms appear to you. Acme is when your disease symptoms are getting much worse. The battle between infectious agent and host has started! 4. Decline phase: Your symptoms are subsided and the host is the champion!! Therefore, the infection crawls away beaten in shame (infection recedes) and your body’s thermostat is reset back to the lower temperature. The reason being is because in order for your body to pick itself back up, blood vessels will have to dilate to lose heat, which is why you sweat and feel cold whenever you get a fever. But these are great signs and symptoms because it is you “breaking through the fever.” 5. Convalescence: the last stage, a.k.a the “healing” stage! During this stage your symptoms go away and you start to feel yourself again with great normal health. When talking about infectious diseases two terms are commonly used, morbidity and mortality. Morbidity is talking about that disease state and its rate of incidences and mortality talks about how many patients died from the disease. Infection Cycles and Disease Transmission An infection cycle can be either complex or simple. The simple infection cycle is called the direct transmission. A direct transmission is when an organism is transmitted directly person to person (ex: sneezing). The complex infection cycle is called the indirect transmission, which has to do with transmitting bacteria through an intermediary (living or nonliving). Fomites are nonliving objects that pathogens can be spread from one person to the next (ex: doorknobs, library books, etc.). But, when an indirect transmission passes through a nonliving object that can as be called, vehicle transmission, where the infectious agent would have to come into contact with fomites and/or through a medium (water, food, or air). Now, there is something called vectors that are living organisms (generally insects) which are involved in the indirect transmission cycle. But there are two OTHER types of transmissions that ONLY deal with indirect transmission through vectors. Horizontal transmission is when a vector transfers a disease from those infected onto a healthy host. The second transmission is, transovarial transmission, which means that the infected vector can pass on the disease onto its eggs. Reservoirs of Infection Reservoirs is a huge factor in the infection cycle. Reservoir is like an animal or environment that usually carries pathogens (ex: rats, chicken, soil, water, etc.). Pathogens survive because of reservoirs. If there were no reservoirs; there would be no more pathogens. Endemic, Epidemic, & Pandemic Now remember, the bacterium Yersinis pestis caused what? If you thought or said the bubonic plague, then you’re right!! So, this bacterium started with an infected rat that was then transmitted to humans by a rat flea! Multiple pandemics of the plague occurred throughout centuries killing a huge chunk of Europe’s population. Moving forward, there are three “emics” we have all heard before, but are finally going to understand what they mean. If you already know these, great job! First is endemic, which is a disease usually found in just one area or group of a community. Second is epidemic, when case(s) of a disease in a community is developed very quickly. Finally, the third is pandemic, when the disease is spread worldwide. Zoonotic Disease Infectious agents will do anything to infect humans, basically their job- infecting hosts. But it is not direct transmission, it’s by indirect transmission. Infections normally afflict animals, but can be transferred to humans (zoonotic diseases). Portals of Entry & Exit How do pathogens enter our bodies? 1. Fecal-oral (defecation & mouth) 2. Skin (epidermis, of course) 3. Respiratory (respiratory tract) 4. Urogenital (conjunctiva, surfaces of genitals & urinary tract) 5. Parenteral (into bloodstream) The way pathogens decide which portal to enter is by their attachment capability, and the reservoir of the organism. Biosafety Procedures It is extremely dangerous to work in a medical facility or lab on pathogens. Of course, there are Microbiologist that work in this kind of field, but there are levels and precautions. Risk group 1: Working with pathogens that don’t really cause horrible diseases to humans. Risk group 2: Working with pathogens of greater potential that group 1. But, there are treatments/vaccines ready for anyone who may get infected. Group 2 deals with tough containment procedures, limited access to lab, and biohazard safety cabinets as well. Risk group 3: Working with pathogens that produce a lethal human disease. But, there are treatments and vaccines for most diseases. Group 3 also has strict limited access to labs and double door air locks so that aerosol transmission does not get through. Risk group 4: Working with very dangerous and exotic pathogens and aerosol transmission is a very high risk as well. Those who work on this level have to wear a one-piece positive pressure suit. The reason being is because if the suit is ever penetrated then pathogens would be pushed AWAY and not sucked into the suit. Host Factors in Disease 1. Age: young and elder are at higher risk of catching an infection. Babies/young kids’ immune systems are still developing & elders’ immune systems are weakening. 2. Host genetic make-up: You know how I said our genes determine whether we’re going to have blue or brown eyes or black or brown hair? Well, our genes have a side job, which is making us more prone to catching an infectious disease! Lovely right? We all have receptors that allow bacteria and/or viruses to bind to them. If we lose a receptor or change one, then that factors towards obtaining pathogens. But there is at least one upside to our genes’ side job. If you have O blood type then you’re more resistant to malaria, so congrats to ya’ll! 3. Host hygiene & behavior: The better your hygiene, the more you are less likely to catch any diseases. But, if you don’t maintain a good hygiene, then you will probably catch a disease...multiple times. The role of behavior is incorporated with the transfer of the disease in a sexual way. 4. Nutrient & exercise: A good immune system is maintained by the help of eating good and regularly exercising. If you don’t eat a lot or starve (DON’T DO THAT) then your stomach is not stoducing as much acid (achlorhydria). Stomach acid is your 1 line of defense against pathogens. If you don’t produce enough, then you’re more likely to catch pathogens like Salmonella and Vibrio cholera. Now, if you don’t exercise as much or at all, then your immune system weakens allowing pathogens to pass by. If you exercise that helps boost your immune system and makes you less capable of catching a cold or something. 5. Underlying noninfectious diseases or conditions: If there are any genetic defects in your immune system, very ill infections, or even medicine required to prevent the rejection of transplant, all will immunocompromise you making you highly acceptable to diseases. Global Change and Emerging Infectious Diseases - Emerging infectious diseases: disease has not been recognized and result in a new organism or organisms that jumped from animal to human. - Reemerging diseases: diseases that were around once upon a time ago, but now have recently reemerged. - Deforestation & urban sprawl: allows insect vectors to be even CLOSER to humans! - Temperature changes and/or drought or excessive rain can affect the distribution of insect/animal vectors. END OF CHAPTER 2! Microbiology: The Human Experience Chapter 5- Cell Biology of Bacteria & Eukaryotes Highlight=Key term Highlight=Important concept Highlight=DON’T FORGET Bacterial Cell: An Overview Most bacteria share these traits: - Complex cell envelope: in other words, the cell wall, cell membrane, & outer layers that protect the environment of the cell. - Small genome: Genomes help pathogens create more of themselves. - Tightly coordinated cell parts: The coordinated action of cell parts working together helps a pathogen reproduce faster. Prokaryote cell shapes: #1 Coccus-round (Diplococci=2, Streptococci=chain, & Staphylococci=cluster) #2 Bacillus-rod like (Diplobacilli=2 & Streptobacilli=chain. There cannot be a staphylobacillus because division only happens along a bacillus’ axis) #3 Spirochetes-spiral (vibrio, spirillum, and spirochete) Model of the Bacteria Cell - Cell membrane or plasma membrane: composed of phospholipids, proteins and very small molecules. The cell membrane helps to prevent cytoplasmic proteins from leaking. It also helps to maintain the concentration gradients of ions. - Cell wall: it is covered with a layer of peptidoglycan, which consists of peptides linking sugar chains. - Periplasm: lays between the outer and inner membranes of the cell. It is a water solution that contains proteins. - Lipopolysaccharide (LPS): type of lipids that attach to long polysaccharides. - Capsule: can be generated by LPS or other sugar chains. It creates a slimy layer that inhibits phagocytosis by white blood cells. Pathogens that do not have their capsule can be more vulnerable to our bodies’ defense. - When you combine together the cell wall, cell membrane, and outer membrane, it composes the cell envelope. The cell envelope contains surface proteins that help bacteria attach to host. - Flagellum: a protein filament that has a motor to help propel the cell find a more suited environment. - Nucleoid: where the chromosomes are located - Fimbriae: helps with attachment - Pilus: has various abilities such as motility and attachment Biochemical composition of Bacteria All cells share these chemical compositions: 1. Water, solvent of life 2. Inorganic ions like K+ and Mg 3. Small organic molecules like lipids and sugars 4. Macromolecules such as proteins and nucleic acids which, hold information and catalyze reactions. Polyamines: included in organic cations and have multiple positively charge amine groups. These polyamines balance out the negative charges of cell DNA and support ribosomes while in translation. Proteins are encoded by a genome and have the ability for expression in cells is called proteome. When you take a closer look at the cells components, you’ll have to break the cell into parts (subcellular fractionation). Bacterial Membrane & Transport Bacterial Membrane Proteins The cell membrane is a 2D lipid bilayer that has a hydrophilic (water soluble) side & a hydrophobic (lipid soluble) side. - Structural support: Proteins that hold together layers of the cell envelope. Some proteins create the base of the cell structure and come out of the cell such as pili and flagella. - Detecting environmental signals: Vibrio cholera, the cause of cholera, when a transmembrane proteins detect acidity and increase in temperature, their amino-terminal domain links to DNA that will stimulate expressions of cholera toxin. - Secreting virulence factors and communication signals: there are some proteins that secrete in order to export toxins. The outer proteins of the membrane turn on cell signaling across the cell envelope. - Transport across the cell membrane: membrane proteins are like bouncers at clubs! The proteins decide what goes into the cell. - Energy storage & transfer: cell maintains different concentrations of molecules inside and out of the cell due to the membrane. Also, energy is storage in gradients and membrane proteins. Transport of Nutrients The way nutrients can cross the membrane is by binding to a transporter protein, called a permease which, delivers nutrients to the other side of the membrane. But there is a problem with the low nutrient concentrations. The way microbes solved this was by evolving transport systems that deal with nutrients inside the cell instead of outside. Passive & Active transport - Passive transport moves molecules from a high to low concentration using no energy. Facilitated diffusion: a type of passive transport that helps carry charged molecules across the membrane. Simple diffusion: another type of passive transport that moves molecules from a high to low concentration (energy is released whenever an ion goes from high to low concentration) Osmosis: has aquaporins which help assist water molecules move from a low to high concentration. (hypertonic: vessel shrinks, hypotonic: vessel expands, Isotonic: no change) - Active transport is used to move molecules AGAINST their gradients! This kind of transport requires a transporter protein & ATP. When energy is used to from one gradient to then move another gradient, that is called coupled transport, and there are two types of coupled transports. First is symport, where two molecules move in the same direction. Second is Antiport, where two molecules move in opposite directions. ABC transport: stands for ATP Binding Cassette which deals with the influx and efflux of ions and molecules. It has two proteins that creates a membrane channel & two cytoplasmic proteins that obtain conserved amino acid that binds to ATP. There is also a substrate- binding protein that binds the substrate. Then the substrate-binding protein goes through the membrane channel and activates the break down (hydrolysis) of ATP into ADP + P in order to get energy to open the channel for the protein to enter. - Siderophores (iron scavengers) are iron-binding molecules and immediately bind to any ferric iron available. The Bacterial Cell Wall & Outer Layers The cell wall is a part of bacteria that supports the cell structure from falling apart. Some bacterial cells have no cell wall due to degenerative evolution. But those that don’t have cell walls usually have additional coverings outside. Cell Wall is a Single Molecule The cell wall helps to prevent osmotic pressure or osmotic shock. Since the cell wall is made up of peptidoglycan (peptide chains of amino sugars), it is the first target for antibiotics. The reason being is because peptidoglycan is not located in eukaryotes. The glycan chains within peptidoglycan contain peptide chains holding only four amino acids. Glycan chains also consist of repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic (NAM) as shown in drawing 1 at the end of this study guide. Peptidoglycan Synthesis is a target for antibiotics In order to synthesize peptidoglycan, there needs to be gene encoding enzymes. Biosynthetic enzymes make a great target for antibiotics. Therefore, the widespread use of antibiotics has led to the evolution of resistant strains. The most common agent for resistance is the beta- lactamase which, chops off any antibiotics. This prevents it from inhibiting transpeptidase. Gram Positive & Gram Negative outer layers - Gram (+) bacteria: a thick cell wall with multiple layers of peptidoglycan that is weaved throughout by teichoic acid, which helps stabilize the cell wall. (phosphate + glycerol = teichoic acid) Teichoic acid helps pathogens attach to their hosts and are known as “bacterial signatures” in the immune system. Also, any bacillus and streptococcus will have a Gram (+) layer. - Gram (-) bacteria: is a thin cell wall with a single layer of peptidoglycan. It has two membranes, an outer and inner. The inner membrane is the lipid bilayer that is selectively permeable. Remember that the inner membrane has hydrophobic & hydrophilic features! The outer membrane aka lipopolysaccharide has three components: Lipid A, core polysaccharide, & O-polysaccharide. Lipid A is an endotoxin that is harmless only if pathogens remain intact. But if pathogen is released then the endotoxin overstimulates the host’s defense causing a lethal endotoxic shock. Lipid A is attached to the core polysaccharide which contains 5 sugars. Lipid A is the reason you/I get fevers! The 5 sugars from the core polysaccharide extend to the O-antigen of the O- polysaccharide. The O-polysaccharide is longer than the cell itself and with both of the polysaccharides it helps a pathogen resist phagocytosis. Oh! Remember the multiple ways a pathogen can enter a host? One of those ways is by changing their shape/form. So, the O- polysaccharide is what helps the morphing of pathogens. An addition to the Gram (-) layer that isn’t located in the Gram (+) are transporters called porins. They allow nutrients to enter the cell such as proteins & sugars. Hint: to help remember these two layers of the membrane think of them as a burger! Gram (+) is only two parts: the cell membrane=bottom bun & peptidoglycan=meat, therefore, there is no top bun. For Gram (-): inner membrane=bottom bun, peptidoglycan=meat, & outer membrane=top bun! Mycobacterial Envelope Mycobacterial is considered to be gram (+) with the exceptions of their envelopes because it is very thick and complexed with extra layers not in gram (+) cells. The structure of a mycobacterial envelope from inside of the cell to out goes: cell membrane, peptidoglycan (cell wall), then capsule. In the mycobacterial envelope, there is a weird and unusual lipid called, mycolic acids which has two hydrocarbon chains as its backbone. Inside the cell wall, mycolic acid and peptidoglycan link up with chains of arabinogalactan. It is composed of galactose and 5 carbon sugar arabinose. The Nucleoid & Bacterial Cell Division A bacteria’s DNA genome usually contains single chromosomes, some linear others circular. But we will mainly be discussing the circular chromosomes. Bacterial DNA is found in the nucleoid; it is held together by DNA-binding proteins. The DNA is read by translation & transcribing to RNA in the cytoplasm to give gene products. During bacterial cell division, it first begins with replicating at the origin bidirectional and then it migrates with two replisomes. Finally, the cell divides into two cells. Specialized Structures of Bacteria There are some structures of bacteria that have specific tasks. The ones particularly important are those for attachment and motility. Pili & Stalks Enable Attachment When a cell has the ability to attach to a substrate with certain structures like pili, it’s called adherence. As bacteria grows, they can decide whether or not to stay at that habitat or go find a new one. In order for the cell to quickly change its environment, the cell requires motility-able to move & relocate. A common structure bacterium uses to attach themselves to substrates are pili. The short pili are fimbriae and the filaments of protein of pili are pilin. There is a different type of pili that attaches male donor cells and female recipients together, it is called sex pili. Rotary Flagella Enable Motility & Chemotaxis Flagella is used to help bacteria and archaea move (generally swim). They are propellers that move the cell forward. The filament of protein monomers of flagella is flagellin. There is a sensory system that most flagellated cells have called chemotaxis. This helps them to swim toward and away from environments. Bacterial Structures for different Habitats - Thylakoids conduct photosynthesis: Phototrophs (photosynthetic bacteria) have to obtain as much light as they can in order to drive photosynthesis. For this to happen, they grow intracellular membranes called thylakoids. - Gas vesicles: To increase buoyancy and stay in high water, aquatic phototrophs possess gas vesicles. These gas vesicles catch and collect other gases like hydrogen or carbon dioxide. - Storage granules: Storage granules are sometimes used as a place to store energy for some bacteria. Storage granules contain glycogen and/or other polymers like PHA (polyhydroxyalkanoates). - Sulfur granules: Bacteria that has a sulfur-metabolism can drop granules of sulfur inside the cytoplasm or globules that are attached outside of the cell. The presence of sulfur could help cells stay away from predation. - Magnetosomes direct motility: Anaerobic bacteria that can swim alongside a magnetic field is a process called magnetotaxis. The tiny magnets that bacteria possess is called magnetosomes. They membrane enclosed crystals of magnetic minerals. Magnetotactic bacteria swim downwards because of the earth’s magnetic field lines are pointing north=downward. The Eukaryotic Cell The larger eukaryotic cells get that more systems of intracellular membranes they have. These membranes create different types of organelles containing vesicles and pockets of membranes. There are enclosed organelles that can have different reactions happen within them. Ribosomes assemble proteins and peroxisomes make hydrogen peroxide. Dynamic Transport Between Membranous Organelles - Lysosome: has enzymes that kill bacteria and process organic material. - Endoplasmic reticulum (ER): it continues from the outer nuclear membrane and from the lumen. The ERs purpose is to sequester substances that have to be held at a low concentration in the cytoplasm. - Exocytosis: vesicles inside the cell fuse with the cell membrane and then the material inside the vesicles are released into the extracellular environment. Endomembrane System - Endomembrane system: several kinds of membrane compartments that has transport networks among them that the ER created. - What makes up the endomembrane system? ER, Golgi apparatus, lysosomes, and peroxisomes. - Rough ER: a type of ER that is part of the endomembrane system. The rough ER is covered with ribosomes that translate their RNA sequence into proteins. - Golgi apparatus: after proteins leave the rough ER, they are secreted into vesicles that migrate to the Golgi apparatus. In this organelle, proteins are told where to go by enzymes that “tag” the proteins. They either are told to go to lysosomes or the cell membrane. The Nucleus Organizes DNA - Nuclear pre complexes: transport material in and out the nucleus. Material like metabolites and small proteins can go right through the nuclear pores. But if it’s large proteins and organelles, they’ll need an active transport. - Nucleolus: inside the nucleus & assembles ribosomes. RNA transcribing of ribosomes also happens in the nucleolus. Mitochondria & Chloroplasts Yield Energy Almost all eukaryotes contain mitochondria, but chloroplast is ONLY found in photosynthetic eukaryotes. Both mitochondria and chloroplasts obtain energy for the cell, but they are not part of the endomembrane system. Mitochondria and chloroplast evolved earlier in life through a type of evolution called endosymbiosis. That is when one cell is inside a bigger cell but it is not digested. It is just a mutualistic relationship between the two. The bigger cell provides protection and the smaller cell inside the bigger one provides energy. - Mitochondria: Has two membranes, an outer and inner membrane. The inner membrane has multiple folding’s called cristae that help increase the surface area. It contains protein complexes for oxidative phosphorylation. The outer membrane has phospholipids kind of similar to bacterial membrane. Mitochondria also has two compartments, the inner space and the matrix. - Chloroplast: converts light energy taken from the sun into ATP and by also decreasing NADPH with a process called the light-dependent reactions. ATP and NADPH are used for decreasing CO^2 to sugar. Chloroplast has three membranes: the outer membrane comes from the eukaryotic cell, the inner membrane is the same as the bacterial cell membrane, and finally the thylakoid membrane, which comes from the bacterial thylakoid membrane. Inside chloroplast is stroma which is like cytoplasm in a bacterial cell. Stroma produces ATP and NADPH. It also has light-independent reactions of CO^2 fixation occurring inside the stroma as well. What the stroma contains is granum and thylakoids. Granum are stacks of disc-liked thylakoids. Cytoskeleton Maintains Shape - Microfilaments: aka actin filaments that can grow and shrink in a controlling manner by polymerization and depolymerization of actin. - Intermediate filaments: a variety of fibrous proteins that help maintain cell shape and strengthen the cell. - Microtubules: are big transporting tubules that can polymerize and depolymerize. They are the ones that that pull apart duplicated chromosomes during mitosis. It also consists of two monomers called, alpha tubulin and beta tubulin and combing both of those monomers together is called a tubulin dimer. Eukaryotic Flagella and Cilia & Pellicle & Contractile Vacuole - Both contains bundles of microtubules inside their thin extensions. Also, they use ATP hydrolysis by dynein (motor protein) in order to generate motion. - Pellicle: has membranous layers that are staying together by protein microtubules. Pellicle gives great flexibility of shape. It can perform endocytosis and phagocytosis. - Contractile vacuole: Its purpose is to get rid of excess water from the cytoplasm. Drawing 1:
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