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| Frage | Antworten |
| What is microbiology? | The study of microorganisms |
| What are microorganisms? | Unicellular organisms that are too small to be seen with the naked eye Microorganisms have limited cell differentiation Microorganisms divide by binary fission instead of mitosis/meiosis |
| What is cell differentiation? | The ability of a cell to divide into different types of specialized cells |
| What are some of the techniques in microbiology? | Cultures, biochemistry, and molecular and genetic techniques |
| What is biochemistry used for in microbiology? | It's used for fast identification of microbes, and is used in medical settings where pathogenic bacteria/viruses would be identified using biochemistry |
| What is the advantage of using molecular and genetic techniques over cultures? | Unlike in culture, you don't need to know the microbe and give it the necessary nutrients and growth medium. You can just identify them using their genetic code. |
| Why is microbiology so important? | It helps us understand the origins and functions of life. |
| List the structures that ALL cells have. | Cytoplasmic membrane, cytoplasm, ribosomes |
| If microbial cells don't have mitochondria, where is energy produced? | In the cell membrane |
| What is a genome | A cell's full complement of genes |
| What is a chromosome? | A genetic element carrying genes essential to cellular function |
| What is a plasmid? | A small, circular piece of DNA that carries non-essential genes Plasmids can be shared between bacteria (same or different species) |
| Why are plasmids so important? | Plasmids may contain genes for antibiotic resistance, which makes them immune to antibiotics |
| What are the 3 categories of microorganisms? | Eukaryotes, prokaryotes, and viruses |
| What are the two major groups of eukaryotic microbes? | Protists and fungi |
| What are protists? | Uni- or multicellular eukaryotic organisms without the capability of differentiation |
| What are the different types of protists? | Protozoa (animal-like), algae (plant-like), and slime and water molds |
| What are the different types of fungi | Yeasts (unicellular), molds (filamentous), and mushrooms (multicellular) |
| What is binary fission? | Unlike mitosis/meiosis, there are no defined stages for DNA replication and division. |
| How are prokaryotes different from the eukaryotes? | Prokaryotes don't have nuclei or organelles, they're generally smaller than eukaryotic cells, have a simple internal structure, divide by binary fission and most are unicellular |
| What are the 2 major groups of prokaryotes? | Bacteria and archaea |
| Are archaea bacteria pathogenic? | No, they don't need to be since they're perfectly fine living in extreme environments. |
| What are viruses? | Viruses are neither eukaryotic or prokaryotic. They're obligate intracellular parasites (can only divide inside a host) and lack independent metabolism |
| Why are viruses so small? | They don't need space for machinery and proteins since they don't have any. They just use the host cell's. |
| What is LUCA? | Last Universal Common Ancestor The ancestor for archaea, bacteria and eukarya |
| Compare the SSU rRNA gene sizes | Prokaryotes - 70S ribosomes; 16S SSU rRNA Eukaryotes - 80S ribosomes; 18S SSU rRNA |
| What are the steps involved in sequencing rRNA genes? | 1: DNA collected from a pure culture 2: The SSU rRNA gene is amplified using the PCR 3: The gene is sequenced 4: Sequence is aligned with the sequences from other organisms |
| What does PCR stand for and what is it? | Polymerase Chain Reaction A technique used to synthesize many identical copies of a short sequence of DNA |
| What are the three domains of life? | Bacteria, Archaea, and Eukarya |
| How do you define species in microbiology? | A species in microbiology is a group of strains that share diagnostic traits, are genetically cohesive, and have a unique recent common ancestor |
| In order to classify species, these guidelines must be followed: | Most characteristics in common >97% sequence similarity in the 16S rRNA gene High degree of genome similarity |
| What type of classification do microbiologists use? | Hierarchical classification King Phyl (COF) Gene S |
| Who is Robert Hooke? | He was the first to describe microorganisms. He never saw bacteria since they were too small to see with his 30x compound microscope |
| What is the first tenet of cell theory? | All living things are made up of cells |
| Who is Antoni van Leeuwenhoek | He was the first to discover bacteria |
| Who is Loius Pasteur? | He discovered that yeasts convert sugar to alcohol in the absence of oxygen (fermentation). He also invented pasteurization |
| What is pasteurization? | A method of gentle but extensive heating, followed by sealing. Keeps food fresh and free from microbes |
| How did Louis Pasteur prove the supporters of spontaneous generation wrong? | He developed a swan-necked flask that trapped particles and microbes in its bend, preventing them from contaminating the solution, but still allowed air to enter the flask |
| What was the main argument against Louis Pasteur's method for keeping his solutions microbe-free? | He first sealed his solutions in airtight jars. His dissenters argued that he must have fresh air entering the solution, so he created the swan-necked flask. |
| List Koch's postulates | Find the suspected pathogen in ALL cases of the disease and absent from healthy animals The suspected pathogen must be grown in pure culture Cells from the pure culture must cause disease in a healthy animal The suspected pathogen must be reisolated and shown to be identical to the original |
| Why do we use agar as a growth medium? | Agar cannot be degraded by most microorganisms It melts at ~97% and solidifies at ~43C (can grow archaebacteria and won't denature) |
| Which method do we use to create a pure culture? | Streak plate technique |
| What is the downside to the streak plate technique? | We can't calculate how many cells there are on the plate since we don't know how many cells we inoculated in the first place |
| Which techniques do we use to determine the quantity of microorganisms? | Spread and pour plate techniques |
| How are spread and pour plate techniques different? | Spread plate - colonies grow on the surface of the medium Pour plate - colonies grow on, in, and under the medium |
| What is the formula for calculating a titre? | titre = # of colonies ------------------ (volume)(dilution) |
| What does cfu stand for? | Colony Forming Unit |
| To be considered statistically significant, plates must have... | Between 30 and 300 colonies >300 is labelled as "too many to count" |
| What are the different types of light microscopy? | Bright-field, phase-contrast, dark-field and fluorescence |
| Define magnification. | The ability to make an object larger |
| Define resolution. | The ability to distinguish two adjacent objects as separate and distinct |
| What is the limiting component of light microscopy? | The wavelength of photons |
| How does wavelength affect resolution? | As wavelength decreases, resolution improves |
| What are some ways to improve contrast for light microscopy? | Staining, phase-contrast, and fluorescence |
| How are basic and acidic dyes different? | Basic dyes have positively charged chromophores, which means they stick to the negatively charged cell surface Acidic dyes have negatively charged chromophores, which means they are REPELLED by the cell surface and instead stick to the background |
| What is a chromophore? | The coloured portion of a dye molecule |
| What specifically does the Gram stain target? | Bacterial cell wall structure |
| What is a gram positive cell? | A cell that retains the primary stain It has a thick layer of peptidoglycan |
| What is a gram negative cel? | A cell that doesn't retain the primary stain and takes the colour of the secondary stain Has a thin layer of peptidoglycan and an outer cell membrane |
| What does a phase-ring microscope do? | It uses a phase ring to improve the contrast of a sample without using stains We can view live cells with phase-ring microscopes |
| What is a dark-field microscope used for? | It's used to observe bacteria that don't stain well The specimen appear as a bright object on a dark background |
| What is a fluorescent microscope used for? | Observing specimen that fluoresce (naturally or artificially after staining with a fluorescent dye) |
| Which techniques can we used to see cells in three dimensions? | Differential interference contrast (DIC), and confocal scanning laser (CSLM) |
| What is an advantage to using CSLM? | We can view cells in layers and reconstruct the cell as a 3D image |
| What are the two types of e electron microscopes? | Transmission electron microscopes (TEM), and scanning electron microscopes (SEM) |
| What are some disadvantages to TEM? | The specimen must be very thin, and it must be stained with heavy metals like lead or uranium |
| How do TEM and SEM differe? | TEM observes internal structures of the cell SEM observes external structures of the cell |
| Even though they're both prokaryotes, how do bacteria and archaea differ? | Bacteria can be either pathogenic or non-pathogenic, while archaea are non-pathogenic because they have no need to live off of other organisms |
| What are the main types of cell shapes? | Coccus (spheres), bacillus (rods), and spirillum (spirals) |
| What are the advantages to small cell size? | Higher surface area/volume ratio, which means faster nutrient exchange and faster growth |
| What is the function of a cell membrane? | Provides a highly selective barrier between the cytoplasm and the environment, and provides a place for building up a concentration of metabolites and waste excretion |
| What is the difference between integral membrane proteins and peripheral membrane proteins? | integral proteins are embedded in the membrane, whereas peripheral proteins are only partly attached to the membrane |
| What is the main different between bacterial and archeaal membranes? | Archaeal membranes don't have fatty acids and instead have isoprenes. Bacterial membranes are made up of phospholipids |
| Besides providing a barrier between the cytoplasm and the environment, what are some functions of the cell membrane? | Holding transport proteins in place, and for generation of the proton motive force |
| What are the three major classes of transport systems in prokaryotes? | Simple transport, group translocation, and ABC system |
| Define simple transport. | Transport using the energy from the proton motive force |
| Define group translocation. | The substance being transported is chemically modified as it's being transported. (This type of transport requires energy) |
| Define ABC transport. | The energy used to drive transport comes from ATP and substances are transported by periplasmic binding proteins |
| Define uniport. | Transport that occurs in one direction only |
| Define symport. | Two substances are transported at the same time across the membrane in the SAME direction |
| Define antiport. | Two substances are transported at the same time across the membrane in OPPOSITE directions |
| What is the periplasm? | The space in between the peptidoglycan and the outer cell membrane in gram negative cells |
| Since gram positives don't have periplasm, what do they use instead? | substrate-binding lipoproteins and ATP-driven transport proteins |
| What does the "ABC" in ABC transport stand for? | ATP-binding cassette |
| What types of proteins are involved in ABC transport? | A solute-binding protein (periplasmic proteins or lipoproteins), integral membrane proteins, and ATP-hydrolyzing proteins |
| What is the major function of t cell walls of archaea and bacterial cells | Protects the cell from osmotic changes |
| How does the cell wall help in pathogenicity? | Help evade the host's immune system Helps bacterium to surfaces (if it can't stick to a surface, it'll just get washed away) |
| How do the cell wall layers differ between gram-positive and -negative bacteria? | Gram-positive have a very thick layer of peptidoglycan Gram-negative have a thin layer of peptidoglycan and an outer membrane |
| How are peptidoglycan molecules linked in gram-positive and -negative bacteria? | In gram-positive, there is an interbridge in between the molecules In gram-negative, the molecules are linked directly |
| What is peptidoglycan made of? | N-acetylglucosamine (NAG), N-acetylmuramic acid (NAM), amino acids, and lysine or DAP |
| Why is peptidoglycan often are target for antibiotics? | We don't have peptidoglycan, so there's no risk of our own cells being attacked |
| What is the peptidoglycan interbridge in gram-positive cells made up of? | Typically made up of five glycine residues, but this may vary between species |
| What makes up gram-positive cell walls? | Peptidoglycan and teichoic acids |
| What are some classes of bacteria that lack peptidoglycan? | Mycoplasmas and thermoplasmas |
| What is another name for the outer membrane of gram-negative bacteria? | Lipopolysaccharide layer (LPS) |
| What is the LPS made out of? | Core polysaccharide, O-poylsaccharide, and lipid A |
| What's so special about lipid A in the LPS layer? | Lipid A is an endotoxin |
| How does penicillin work to prevent bacterial cell walls from synthesizing? | It physically blocks the reaction that powers crosslinking of peptidoglycan molecules |
| Where does the crosslinking of peptidoglycan molecules occur? | The periplasm |
| What do archaeal cell walls have instead of peptidoglycan? | Pseudomurein |
| How is pseudomurein different from peptidoglycan? | Instead of N-acetylmuramic acid, pseudomurein has N-acetylalosaminuronic acid |
| What makes archaeal cell walls immune to lysozymes? | Lack of peptidoglycan. Lysozymes target peptidoglycan, so by not having this molecule, archaeal cells won't be targeted. |
| Other than cell walls made of pseudomurein, what other wall structure do archaeal cells have? | S-layers are the most common type |
| Why are archaeal cells resistant to lysozymes and penicillin? | They don't have peptidoglycan |
| What is a proroplast? | The cytoplasm and the plasma membrane |
| What are the main functions of proteins? | Enzymes, transport proteins, transport proteins, and structural proteins |
| What is the nucleoid? | The region in the cytoplasm where DNA is contained |
| What are some uses for capsules and slime layers? | Assist in attachment to surfaces, protect against phagocytosis, and resist desiccation Basically, they help the cell avoid the host's immune system |
| What is the difference between capsules and slime layers? | Slime layers are thinner than capsules. Both are charged, which repels the immune system cells. |
| What are fimbriae? | Filamentous proteins structures that enable organisms to stick to surfaces or form membranes |
| What are pili? | Filamentous protein structures like fimbriae, but are longer. Their purpose is to create a bridge for two cells to share their DNA. One type (Type IV) are involved in motility |
| What are some storage structures that can be found in the cytoplasm? | Carbon storage (PHB for lipid storage and glycogen), polyphosphates, sulfur globules, and magnetosomes |
| Why do some cells have gas vesicles? | Gas vesicles in photosynthetic organisms found in water are used as floatation devices. This is so they have access to sunlight |
| What are endospores? | Highly differentiated cells that are resistant to heat, harsh chemicals, and radiation. The dormant stage of a bacterial cell. This stage can last for YEARS. |
| Do archaeal cells form endospores? | No, they don't need it since their normal vegetative form is capable of handing extreme conditions. Bacterial cells are not, so some of them form endospores. |
| Which type of bacterial cell form endospores? | Only some gram-positives can produce endospores |
| What are the protective features of an endospore? | Spore coat and cortex protect agains chemicals, enzymes, physical damage and heat Two membranes provide permeability barriers against chemicals The core is dehydrated (so the endospore doesn't boil in high temps), and contains Ca-dipicolinic acids and SASPs to protect against DNA damage |
| What are the stages of endospore formation? | Stage 1: DNA replication Stage 2: The cell is divided into 2 unequal compartments called the forespore and a mother cell. All the DNA goes into the forespore Stage 3: Mother cell engulfs the forespore. The forespore has two membranes surrounding it Stage 4: Thick layers of peptidoglycan form between the two membranes to form the cortex Stage 5: Protein coat forms Stage 6: Endospore matures Stage 7: Mother cell disintegrates and mature spore is released |
| Can you see flagella with normal staining? | No, you need to use a different kind of staining process |
| Define monotrichous. | A single flagellum at or near one end of the cell |
| Define amphitrichous. | Flagella at opposite ends of the cell |
| Define lophotrichous | Multiple flagella in a single tuft on a cell |
| Define peritrichous | Flagella distributed all over a cell |
| What is the basic structure of a flagellum? | Filament, hook, and basal body |
| What is a flagellum's filament section made out of? | Flagellin |
| What layers must a basal body of a flagellum pass through? | L ring - LPS layer (in gram-negatives only) P ring - peptidoglycan MS ring - membrane C ring - cytoplasm |
| What powers a flagellum? | Proton motive force, which is generated by mot proteins. |
| What do mot proteins do? | They form a channel that allows protons to move inside the cytoplasm, and provides energy for a flagellum to turn |
| How do flagella move? | Like a propeller (eukaryotic flagella use a wave-like motion) |
| Besides flagellar movement, what is another type of locomotion for cells? | Gliding, which requires slime to be excreted, a type IV pili and gliding-specific proteins |
| Define taxis. | Directed movement in response to physical or chemical gradients |
| Define chemotaxis | Movement in response to chemicals |
| Define phototaxis | Movement in response to light |
| Define aerotaxis | Movement in response to oxygen |
| Define osmotaxis | Movement in response to osmotic pressure (ions) |
| Define hydrotaxis | Movement in response to water |
| How big are prokaryotic cells, typically? | 0.2 to 2.0 microns |
| What is a macronutrient? | Elements required in large amounts because they're needed to build macromolecules C, H, O, N, P, and S are the organic macronutrients |
| What are the inorganic macronutrients needed by cells? | K, Mg, Ca, and Fe |
| What is the main purpose of inorganic macronutrients? | They're often metabolic cofactors (something needed for enzymes to work properly) |
| When preparing culture media, which macronutrients should be considered? | All of them. C HOPKNS CaFe Mg |
| What are micronutrients? | Elements that are required by the cell in small amounts (trace elements). They usually serve as cofactors for enzymes. Mn, Zn, Co, Ni, Cu, Mo, and Se. |
| Which is the most abundant element in the cell (by mass)? | Carbon |
| What are growth factors? | Small organic molecules that are required for growth. If an organism can't synthesize a growth factor, then you must add it to the medium to grow that microbe in the lab |
| What are the three types of growth factors? | Amino acids, purines and pyrimidines, and vitamins |
| Which are purines and which are pyrimidines? | Purines: adenine and guanine Pyrimidines: thymine, cytosine, and uracil |
| What are vitamins? | Small molecules used to make organic cofactors |
| What is a limiting nutrient? | A nutrient that is in relatively low concentration compared to other nutrients. When it runs out, growth stops even though other nutrients are still present. |
| What is assimilatory sulfate reduction? | The reduction of sulfates to synthesize sulfur-containing compounds |
| What are heterotrophs? | Organisms that use organic carbon (obtained from another organism) |
| What are autotrophs? | Organisms that use inorganic carbon (CO2) as their sole source of carbon Photosynthetic organisms are autotrophs |
| What is a defined medium? | A type of medium where the exact chemical composition is known. |
| What is a minimal medium? | A medium where only the required nutrients are provided. If the organism can make the nutrient itself, it won't be provided. |
| What is a complex medium? | Usually identified by the lack of chemical formulas and is created from meat or yeast extracts. The exact chemical composition for this type of medium is unknown. T-soy plates are an example of this. |
| What is a differential medium? | A medium where organisms react differently, allowing us to distinguish them from each other. |
| What is a selective medium? | A medium that contains ingredients that inhibit the growth of unwanted microbes. This medium only allows specific microbes to grow. Example: only halotolerant bacteria will grow on a medium with a high salt content |
| What is an enriched medium? | A medium that contains added special nutrients to encourage growth of "picky" bacteria |
| What is metabolism? | The sum of all the chemical reactions that occur in a cell |
| What is catabolism? | Energy-releasing metabolic reactions (produce energy) |
| What is anabolism? | Energy-requiring metabolic reaction (consume energy) |
| What are chemoorganotrophs? | Organisms that get energy from organic chemical reactions (heterotrophs) |
| What are chemolithotrophs? | Organisms that get energy from inorganic chemical reactions (autotrophs) |
| What are phototrophs? | Organisms that get energy from light (autotrophs) |
| What is generation time? | The time required for microbial cells to double in number (with binary fission) |
| Bacteria have ____ generation times compared to eukaryotic microbes. | Shorter |
| What type of growth is shown by bacteria when there are no limiting factors? | Exponential growth |
| How do you calculate the number cells present in a culture after a period of exponential growth? | |
| How do you calculate growth rate (k)? | |
| How do you calculate generation time? | g = 1/k |
| What is a batch culture? | A closed system microbial culture of fixed volume |
| What are the four phases that characterize the growth curve for cells in a closed system? | Lag phase, exponential phase, stationary phase, and death phase |
| What is the lag phase? | The interval between inoculation of a culture and the beginning of growth |
| What is the exponential phase? | The cells in this phase are typically in the healthiest state; growth continues |
| What is the stationary phase? | Cells are still alive, but there is no growth because either an essential nutrient is used up, or waste product has accumulated (In a closed system, there's no way to get rid of wastes) |
| What is the death phase? | If incubation continues after stationary phase, cells will eventually die (Not all bacteria will die, some will form spores or cysts) |
| What is a continuous culture? | An open system of microbial culture of fixed volume (Fresh medium comes in all the time and the wastes are discarded) |
| What is the most common type of continuous culture device? | Chemostat |
| What is dilution rate? | The rate at which fresh medium is pumped in, and spent medium is pumped out. |
| What are some ways to count microbial cells? | Petroff-Hausser counting chamber (microscope slide with a grid printed on it) Flow cyclometer (used with liquid samples) |
| What are the limitations of microscopic counts? | You can't tell the difference between live and dead cells Small cells can be missed Precision Need a phase-contrast microscope if a stain is not used Cell suspensions of low density is hard to count Motile cells need to be immobilized Debris can be mistaken for cells Cells may move or form clumps |
| What is viable cell counts? | Measurements of only LIVING cells |
| What is the great plate anomaly and what causes this? | Microscopic counts of natural samples have way more organisms than those from plate samples. Microscopic methods count dead cells, while viable methods do not Different organisms have different requirements for growth We don't know the specific requirements for all organisms |
| What are indirect methods of counting cells? | Spectophotometry, measurement of dry cell weight or specific components of cells |
| What method of counting cells does not disturb the sample? | Spectophotometry/turbidity measurements |
| What is one problem with turbidity measurements at high concentrations, and how can we avoid it? | At higher concentrations, the actual turbidity graph will plateau off and the theoretical graph won't follow it. To combat this, we can use dilutions |
| What are some issues with optical density? | Has a finite linear range of measurement There can be no clumps or biofilms The cuvette can't have any scratches (it diffracts light) If the cells are at a high density, the culture must be diluted |
| Define cardinal temperature | The minimum, optimum, and maximum temperatures at which an organism grows. These differ with each organism. |
| Define minimum temperature | The lowest possible temperature at which an organism can function at. The cell membrane gels, which slows down transport processes enough that the organism is unable to grow. |
| Define optimum temperature. | The temperature at which an organism's enzymatic reactions are occurring at the fastest rate. |
| Define maximum temperature. | The highest temperature at which an organism can survive without its proteins being denatured, the cytoplasmic membrane collapsing, and thermal lysis occurring. |
| What are the different temperature classes of microorganisms? | To be classified as one of these, the organism's optimum temperature must fall under that class. Psychrophile - low (<20C) Mesophile - midrange Thermophile - high (45C-80C) Hyperthermophile - extremely high (>80C) |
| Which temperature class do pathogens fall under? | Mesophile, because our body temperature is their optimum temperature. |
| Define extremophiles. | Organisms that grow under very hot or very cold conditions. |
| What is the difference between a -phile and a -tolerant? | A -phile has an optimum temperature at that class, and a -tolerant can survive at that temperature, but it won't be able to function at the fastest/best rate. |
| What are some adaptations that psychrophiles have for living in the cold? | Enzymes that functions optimally in the cold temperatures Modified cytoplasmic membranes High concentrations of UNSATURATED fatty acids |
| Which would work better in the cold: unsaturated or saturated fatty acids? | Unsaturated, because saturated fatty acids freeze at higher temperatures. |
| What are some adaptations that thermophiles have for living in the heat? | Modified enzymes and proteins so that they don't denature in the heat Modified cytoplasmic membranes (high concentration of saturated fatty acids, or lipid monolayers instead of bilayers) |
| What are the classes of microorganisms based on pH levels? | Acidophiles - grow best at low pH (<6) Alkaliphiles - grow best at high pH (>9) Most organisms are neutrophiles |
| Are acidophiles and alkaliphiles actually different from neutrophiles? | No, they just have a cytoplasmic membrane that can hold up better in their environment. Their internal structures are very similar to neutrophilic cells. |
| Define water activity (Aw) | The amount of water that is interacting with ions and polar compounds in solution. |
| Define halophilic. | Organisms that grow best at high salt concentrations/reduced water potential. |
| What is the difference between halotolerant and extreme halophiles? | Halotolerant organisms can function at in environments with reduced water activity, but prefer low salt concentrations. Extreme halophiles NEED very high salt levels to function. |
| Define osmophiles. | Organisms that grow best at environments with a high sugar content. |
| Define xerophiles. | Organisms that are able to grow in very dry environments. |
| What are the different classes of microorganisms based on oxygen? | Obligate aerobes, strict anaerobes, facultative anaerobes, aerotolerant anaerobes, and microaerophiles. |
| Define obligate aerobe. | An organism that needs oxygen to live. |
| Define strict anaerobes. | Organisms that don't need and may even be KILLED by oxygen. |
| Define facultative aerobes. | Organisms that can live with or without oxygen. They prefer to use oxygen though. |
| Define aerotolerant anaerobe. | Organisms that can tolerate and grow in the presence of oxygen, but do not use it. |
| Define microaerophile. | Organisms that can only survive in low concentrations of oxygen. |
| What would you need in order to grow anaerobic microbes? | Reducing agents, which are chemicals that can be added to culture media to reduce oxygen. An airless space, replaced with an inert gas such as nitrogen or argon. |
| What are some toxic forms of oxygen that can be formed in the cell? | Superoxide anion (O2-) Hydrogen peroxide (H2O2) Hydroxyl radical (OH*) |
| What are some enzymes that can convert toxic forms of oxygen to harmless water? | Catalase, peroxidase, superoxide dismutase, and superoxide reductase. Obligate anaerobes don't have these enzymes, which makes it impossible for them to live in the presence of air. Microaerobes don't have these either, but they're able to use up oxygen before it enters the cell. |
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