MMG 201 exam LO's.pdf

Chapter 2: Invisible World Section 2.1 Properties of Light Identify and define the characteristics of electromagnetic radiation (EMR) used in microscopy ○ In terms of the behavior of light, define wavelength - The distance between the apex of two waves. ○ De...

Chapter 2: Invisible World Section 2.1 Properties of Light Identify and define the characteristics of electromagnetic radiation (EMR) used in microscopy ○ In terms of the behavior of light, define wavelength - The distance between the apex of two waves. ○ Describe what the electromagnetic spectrum of visible light looks like, and which color is the longer and shorter wavelength - The spectrum goes from red (longer) to purple (shorter) ○ Explain how lenses are used in microscopy to manipulate visible and ultraviolet (UV) light ○ Describe how refraction is useful in lenses - Refraction is how light waves change direction as they enter a new medium (often due to  moving slower, as they enter a medium with a higher refractive index. To combat this, two lenses are used by compound microscopes, an objective lens (4x, 40x, or 100x) and an ocular lens (10x), which flip the image upside down and backward. ○ Explain magnification and resolution - Magnification makes images bigger. Total magnification is calculated by multiplying the ocular and objective lens magnifications. Resolution is how well two points can be defined on an image. Section 2.2 Peering Into the Invisible World Describe historical developments and individual contributions that led to the invention and development of the microscope ○ Describe the microscope created by van Leewenhoek - Leewenhoek created the simple microscope. It used one lens. Compare and contrast the features of simple and compound microscopes ○ Distinguish a simple from a compound microscope - Compound microscopes have multiple lenses, simple microscopes have one. Section 2.3 Instruments of Microscopy Identify and describe the parts of a brightfield microscope ○ If provided with a diagram, be able to identify and give the function of the ocular lens, objective lens, stage, illuminator of a brightfield microscope.  ○ Explain why/how immersion oil is useful in microscopy. - Immersion oil is used to fill the gap between a specimen and the glass slide that contains it. This is important because the oil has a similar refractive index to the glass slide, diminishing the level of refraction that will occur as light passes through to the specimen. Otherwise, the light would pass through the glass to the air to the specimen, and since air has a much different refractive index, it would create visible refraction. Calculate total magnification for a compound microscope ○ If given the magnifications of the ocular and objective lenses, be able to state how the total magnification is calculated (you will not need a calculator for the exam) - Ocular x Objective = Total Describe the distinguishing features and typical uses for various types of light microscopes, electron microscopes, and scanning probe microscopes ○ Review but do not memorize details about darkfield, phase-contrast, differential interference contrast, fluorescence, confocal, two photon microscopes. Do not memorize the three tables at the end of this section. ○ For electron microscopes, explain what is used in place of visible light, and what is used for lenses in place of glass. ○ Light Microscopes: Use light to visualize images. ○ Electron Microscopes: Use short-wavelength electron beams instead of light. Instead of lenses, this uses Electromagnetic lenses to generate magnetic fields and control the path of electrons. Section 2.4 Staining Microscopic Specimens Differentiate between simple and differential stains ○ Describe the difference between a simple stain and a differential stain - In simple staining , a single dye is used to emphasize particular structures in the specimen. A simple stain will generally make all of the organisms in a sample appear the same color, even if the sample contains more than one organism. - In contrast, differential staining distinguishes organisms based on their interactions with multiple stains. In other words, two organisms in a differentially stained sample may appear to be different colors. - In class, Dr. Miller said that “differential stains are used to differentiate” or something to that effect. This is helpful for me when recognizing that gram-stains, endospore stains, capsule, and flagella stains are all differential. Describe the unique features of commonly used stains ○ Distinguish between a positive and negative stain - A positive dye will be absorbed by the cells or organisms being absorbed, adding color to objects of interest to make them stand out against the background. Because cells typically have negatively charged cell walls, the positive chromophores in basic dyes tend to stick to the cell walls, making them positive stains. Thus, commonly used basic dyes such as basic fuchsin, crystal violet, malachite green, methylene blue, and safranin typically serve as positive stains. - A negative stain, which is absorbed by the background but not by the cells or organisms in the specimen. Negative staining produces an outline or silhouette of the organisms against the colorful background. The negatively charged chromophores in acidic dyes are repelled by negatively charged cell walls, making them negative stains. Commonly used acidic dyes include acid fuchsin, eosin, and rose bengal. Explain the procedures and name clinical applications for Gram, endospore, acid-fast, negative capsule, and flagella staining ○ Explain what happens in the steps of the Gram staining procedure for the primary stain, mordant, decolorizing agent, and counterstain 1. First, crystal violet, a primary stain, is applied to a heat-fixed smear, giving all the cells a purple color. 2. Next, Gram's iodine, a mordant, is added. A mordant is a substance used to set or stabilize stains(Make primary stain attach to  peptidoglycan) or dyes; in this case gram's iodine acts like a trapping agent that complexes with the crystal violet-iodine complex clump and stay contained in thick layers of peptidoglycan in the cell walls. 3. Next a decolorizing agent is added, usually ethanol or an acetone/ethanol solution. Cells that have thick peptidoglycan layers in their cell walls are much less affected by the decolorizing agent; they generally retain the crystal violet dye and remain purple. However, the decolorizing agent more easily washes out the dye of cells with thinner peptidoglycan layers, making them again colorless. 4. Finally, a secondary counterstain, usually safranin, is added. This stains the decolorized cells pink and is less noticeable in the cells that still contain the crystal violet dye. ○ Be able to evaluate and interpret the results/outcome of a Gram staining procedure based on the steps taken/not taken - Older bacterial cells may have damage to their cell walls that causes them to appear gram-negative even if the species is gram-positive. So it's better to use fresh bacterial cultures. - Leaving on a decolorizer for too long can affect the results. - Heat fixing a sample to a slide will lyse the cells, killing them and preventing the cells from holding the stain. - If the mordant is forgotten, no positive stains will be shown. - If the decolorizing agent is forgotten, the whole slide will appear with the color of the mordant. - If the counterstain is forgotten, the cells that did not take up the primary stain would be very hard to see. ○ Provide the colors for Gram-negative and Gram-positive cells at the end of the Gram staining procedure The purple, crystal violet stained cells are referred to as gram-positive cells, while the red, safranin-dyed cells are gram negative. Additionally, other cells, such as eukaryotic cells, will also become pink/red safranin stained. -Purple (Picked up primary stain) - Gram Positive -Pink (Picked up secondary stain) - Negative  Since primary stain sticks to peptidoglycan, any cell that doesn't have enough peptidoglycan can be decolorized by a decolorized agent and appear pink at the end (because a secondary stain was added) ○ Describe what the acid-fast stain is used for, and what endospore, flagella, and capsule stains show (do not memorize table 2.4.1 or Preparing Specimens for Electron Microscopy) Acid fast staining is a differential staining technique. It's used to differentiate between two types of gram-positive cells: those that have waxy mycolic acid in their cell walls, and those that do not. Endospore stain is used to distinguish organisms with endospores from those without; used to study the endospore. Bacterial endospores function in a similar manner to the cystic form of a trophozoite. They encase the bacteria and allow it to survive in less than optimal conditions. Capsule stain used to distinguish cells with capsules from those without. Capsules are a virulence factor in bacteria and are a glycocalyx structure. They can be dense or slimy. Flagella stain used to view and study flagella in bacteria that have them. Flagella are used to allow the microbe to move. Chapter 3: The Cell Section 3.1 Spontaneous Generation Explain the theory of spontaneous generation and why people once accepted it as an explanation for the existence of certain types of organisms. ○ Briefly state what the theory of spontaneous generation says. The theory of spontaneous generation states that life can arise from non-living matter. There were many reasons people believed the theory. It was before the invention of microscopes so people were still not familiar with the idea of microbes and were not aware of their involvement in decay and fermentation.  Based on the experiments conducted back then and from what people had seen, supported the theory of spontaneous generation. Such as living things emerging from decaying matter. However, it was because the experiments did not do it completely sealed so the bacteria got into the experiments. Redi’s experiment was also not widely known and accepted. Explain how certain individuals (van Helmont, Redi, Needham, Spallanzani, and Pasteur) tried to prove or disprove spontaneous generation. (Focus on Redi and Pasteur) ○ Explain in a few sentences how Francesco Redi proved that maggots did not arise from meat, but from flies. Redi His experimental setup consisted of an open container, a container sealed with a cork top, and a container covered in mesh that let air in but not flies. Maggots only appeared in the open container. However, maggots were also found on the gauze of the gauze covered container. Which proved that maggots did not arise from meat but from flies. He disapproved of spontaneous generation. ○ Describe how Pasteur’s swan neck flask experiment helped disprove the theory of spontaneous generation. Louis pasteur He made a series of flasks with long twisted necks. Known as swan neck flasks. In which he boiled broth to sterilize it. His design allowed air inside the flask to be exchanged with air outside, but prevented the introduction of any airborne microorganisms, which would get caught in the twists of the flask's neck. He correctly predicted that the sterilized broth inside the flask would remain sterilized as long as the neck was still intact. If broken the broth would become contaminated. Section 3.2 Foundations of Modern Cell Theory Explain the key points of cell theory and the individual contributions of Hooke, Schleiden, Schwann, Remak, and Virchow  ○ State who first used the term “cell”, and what method was used to make this observation. English scientist Robert Hooke first used the term cell in 1665 to describe the small chambers within the cork that he observed under a microscope of his own design. The section of cork resembled honey-combs. Explain the key points of endosymbiotic theory and cite the evidence that supports this concept The endosymbiotic theory is a widely accepted scientific theory that explains the origin of certain organelles in eukaryotic cells, particularly mitochondria and chloroplasts. The theory proposes that these organelles originated as free-living prokaryotic organisms (bacteria) that were engulfed by a host cell. Over time, a symbiotic relationship developed between the host cell and the engulfed organisms, leading to the engulfed bacteria becoming permanent residents within the host cell, evolving into the organelles we see today. Based on the chloroplasts ability to produce independently, russian botanist konstantin suggested that chloroplasts may have originated from ancestral photosynthetic bacteria living symbiotically inside a eukaryotic cell.  Additionally, mitochondria and chloroplasts both have their own 70s ribosomes, similar to bacteria, their own genetic information, and have a double membrane which would have been engulfed during the endosymbiotic event. Explain the contributions of Semmelweis, Snow, Pasteur, Lister, and Koch to the development of germ theory The germ theory of disease is a fundamental scientific theory that states that many diseases are caused by microorganisms, such as bacteria, viruses, fungi, and parasites. These microorganisms, also known as "germs," can invade and multiply within a host organism, leading to illness. In 1847 Semmelweis demonstrated that handwashing reduces puerperal infections. In 1854 Snow demonstrated that cholera bacteria were transmitted in contaminated drinking water. In 1856 Pasteur discovered microbial fermentation while studying the causes of spoilage in beer and wine. In 1862 Pasteur disproved spontaneous generation with a swan-neck flask experiment. In 1867 Lister began using carbolic acid as a disinfectant during surgery. 1876-1906 Koch and his workers determine causative agents for many bacterial infections. Section 3.3 Unique Characteristics of Prokaryotic Cells Explain the distinguishing characteristics of prokaryotic cells ○ Describe general features of prokaryotic cells mentioned in the first 4 paragraphs - They lack a nucleus - No membrane bound organelles - They are small in size - Most prokaryotes have a rigid cell wall - Plasma membrane made of lipid bilayer - 70s ribosomes (similar to the ribosomes of mitochondria/chloroplasts in eukaryotes) - The genetic material is usually a single circular DNA molecule - Reproduce by binary fission  - Flagella (optional) help with movement - Pili are hair-like projections that allow prokaryotic cells to attach to surfaces. Sex pili - Some cells have a capsule, which helps the bacteria evade the host immune system, adhere to surfaces, and resist desiccation. - Some bacteria can form endospores. Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology ○ Be able to recognize common prokaryotic cell arrangements (also review Week 2 slides from class).  ○ Briefly describe the effects of placing a cell in isotonic, hypertonic, and hypotonic solutions. Isotonic: Nothing happened, the concentration is the same outside and inside the cell Hypertonic: Concentration Higher Outside, water in the cell wanted to go out Cell Membrane shrinks and detaches from cell wall Hypotonic: Concentration Higher in the cell, water outside keeps trying to get in the cell Cell swell and lysis Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function ○ Briefly explain how the cell wall is involved in cell morphology. The cell wall determines the shape of bacteria Cell wall chemical structure: Bacteria - Peptidoglycan (Gram-positive has thick layer on top, gram-negative has thin layer in between plasma membranes and liposaccharides) Archaea - Pseudopeptidoglycan or glycoproteins or polysaccharide or S-layer protein Cell wall function Give Structure support, prevent prokaryotes against osmotic pressure Give Protection, shield cells from the external environment and give cell stability ○ Describe the location and function of the nucleoid, plasmids, ribosomes, and endospores. Nucleoid Prokaryotes' chromosomes are: ○ Unpaired ○ Circular ○ Not bound by complex nuclear membrane Where chromosomes concentrate in cell Interact with NAPs(nucleoid-associated proteins) that assist the organization & packaging of chromosomes ○ Bateria: NAPs function like histones  ○ Archaea: NAPs or histones-like DNA organizing proteins organize nucleoid Plasmids DNA that is not part of chromosomes Smaller Circular Double-stranded DNA molecules More common in bacteria but are also found in algae and eukaryotes Carry genes that give traits like antibiotic resistance - Important to survival of organisms Ribosomes Found in Cytoplasm Prokaryotes size 70S Function as producing proteins and enzymes cells need Endospores To protect bacterial genome in harsh environment Kinda like cyst in protozoa Sporulation: From bacteria to Endospore ○ Describe in a general way what inclusions are used for. (Don’t memorize specific inclusions) Inclusion is used for storing excess nutrients ○ Be able to recognize features of a plasma membrane (fig. 3.2.1) ○ Distinguish simple diffusion from active transport  Simple diffusion: No ATP required, Substances(small, like O2 or H2O) go from high concentration to low concentration until the balance is met (They may pass through the membrane, like small molecules, or flow through an intermembrane protein) Active transport: Required ATP, for all ions. Ions go to a more concentrated place. So from low to high (This is often facilitated by membrane proteins, like ion-gated channels) ○ State the major components and function of peptidoglycan. Major Components Glycan chain ○ Composed by NAG and NAM ○ Long chain in each layer ○ Backbone of peptidoglycan Peptide Cross-linked ○ Short peptide chain linked between glycan chain ○ Provide strength and hardness of peptidoglycan layer ○ Reinforcing cell wall structure Functions Give structural support, help maintain cell shape and prevent cells from lysis from osmotic pressure Protect bacteria from environmental stresses Target of antibiotic, ex) penicillin targets synthesis of peptidoglycan and makes bacteria die from osmotic pressure ○ Compare the cell wall structures of Gram-negative and Gram-positive cells, especially noting differences in the membranes, arrangement of peptidoglycan. Gram-Positive Thicker peptidoglycan layer (30 nm) Teichoic Acid (TA) stabilizes peptidoglycan by being harder ○ Can also bind to certain proteins on the surface of the host cell - increasing the infection ability Gram-Positive Acid-Fast bacteria ○ Have an enteral layer of waxy mycolic acid ○ Name Acid-Fast because need acid-fast stain to dye mycolic layer Gram-Negative Thinner peptidoglycan layer (lower than 4nm)  Second lipid bilayer (outer membrane) ○ Attached to peptidoglycan by murein lipoprotein ○ Outer side of outer membrane has lipopolysaccharide (LPS) function as endotoxin in infection ○ Compare a capsule with a slime layer. 2 Types of Glycocalycces structure outside bacteria cell wall Capsule: ○ Usually composed of polysaccharides or proteins ○ An organized layer located outside cell wall ○ Give microbes ability to cause disease (Capsule make white cells more difficult to engulf/kill) Slime layer ○ May composed of polysaccharides, glycoproteins and glycolipids ○ Less tightly organized and only loosely attached to cell wall ○ More easily to wash off ○ Briefly describe the function of fimbriae, pili, and flagella Fimbriae Enable cell to attach to surface of other cells ○ Important to adhere to host cell bc it helps colonization, infectivity and virulence ○ Important for biofilm formation Pili Aid in attachment of surfaces Mainly used to transfer DNA between bacteria cells, exchange parts of their respective genomes Flagella Mainly help in movement, to leave harsh environment or go to good environment Flagella may differ in size, number, or arrangement Flagella need a specific differential stain to be identified Compare and contrast the distinguishing characteristics of bacterial and archaeal cells ○ Cell wall Bacteria: Peptidoglycan  Archara: Polysaccharides, Glycoproteins, pseudopeptidoglycan or S-layer proteins ○ Membrane Lipids Bacteria: ester-linked phospholipids Archaea: ether-linked ○ Genome characteristics Bacteria: Lack histones Archara: Contains histones ○ Habitat Bacteria: Almost everywhere Archaea: Usually in very extreme environment ○ Pathogenic Bacteria: Occasionally pathogenic Archaea: None are found pathogenic ○ Bacteria are occasionally pathogenic Section 3.4 Unique Characteristics of Eukaryotic Cells Explain the distinguishing characteristics of eukaryotic cells ○ Recognize that cell morphologies of eukaryotic cells can vary widely and are highly dependent upon the environment in which the microorganism lives ○ Describe internal and external structures of eukaryotic cells in terms of their physical structure, chemical structure, and function ○ External – Optional; flagella and cilia for movement and attachment (respectively) ○ Cell wall – Optional for eukaryotes, many may have it based on their environment and they may differ as a result (ex: floating plant or plant that needs to grow up); ○ Plasma membrane – phospholipid bilayer contains membrane proteins and cholesterol/sterols for rigidity, semi-permeable to allow only some things in ○ Internal – Endomembrane system: Endoplasmic Reticulum (rough contains ribosomes to synthesize membrane proteins in emergency, smooth can detoxify or preform lipid synthesis), Golgi apparatus (uses ribosomes from RER to make glycoproteins for outside of cell, may do  the same for lipids from the SER to make lipoproteins); Ribosomes (RER, free (cytoplasmic) to maintain homeostasis, mitochondrial and chloroplast to help generate ATP (perform cellular respiration or photosynthesis), the free and RER ribosomes are 80s, the others are 70s due to bacterial origin (theory of endosymbiosis); vacuoles to engulf, lysosomes to digest, peroxisomes to contain hydrogen peroxide and catalase to break down hydrogen peroxide. Identify and describe structures and organelles unique to eukaryotic cells ○ Briefly describe the function of the nucleus, cytoskeleton, mitochondria and chloroplasts, and endomembrane system. Nucleus holds genetic information in the nucleolus. It is surrounded by the ER so that it can relay information to it quickly. The cytoskeleton goes throughout the cytoplasm and acts as a road for ribosomes and other organelles as well as playing a role in cell division and the maintenance of cellular structure. Compare and contrast similar structures found in prokaryotic and eukaryotic cells ○ Describe differences in the cell structures of bacteria and eukaryotes for the nucleus, cell division, and membrane-bound organelles Prokaryotes do not have a nucleus but rather have a nucleotide region, prokaryotic cell division is by binary fission, eukaryotic cell division is by mitosis/meiosis. Prokaryotes do not have membrane-bound organelles. In both: Plasma membranes, free/cytoplasmic ribosomes, cytoplasm, In only eukaryotes: nucleus, ER, Golgi, 80s ribosomes, mitochondria/chloroplasts In only bacteria: capsule, plasmids, peptidoglycan, ○ Differentiate the structures in prokaryotic and eukaryotic cells that contain the chromosome, compose the cell wall, and provide motility. Eukaryotes: nucleolus, varying composition of cell wall, motility with flagella or cilia Prokaryotes: nucleotide region (and additional plasmids), peptidoglycan, flagella, or pili Describe the processes of eukaryotic mitosis and meiosis, and compare to prokaryotic binary fission  ○ Do not learn individual steps in mitosis or meiosis, just understand the general differences between eukaryotic and prokaryotic cell proliferation cycles. Eukaryotic can either mix DNA (meiosis) or produce an exact copy (mitosis). Prokaryotes go through binary fission and produce an exact copy. Chapter 4: Prokaryotic Diversity Section 4.1 Prokaryote habitats, relationships, and microbiomes Identify and describe unique examples of prokaryotes in various habitats on earth ○ Recognize that prokaryotes are ubiquitous Prokaryotes can be found everywhere because they are extremely resilient and adaptable. Most of them are metabolically flexible, which means they might switch from one energy source to another depending on the availability of the sources, or from one metabolic pathway to another. ○ Be able to describe a prokaryote that may live anywhere on Earth when environmental conditions are provided, using appropriate terminology (e.g., soil-dwelling microbe that lives near the surface is most-likely aerobic/aerotolerant, perhaps a mesophile, and probably a neutrophile) Aerobic - needs O2 to survive Aerotolerant - can survive in presence of O2 Mesophile - prefers moderate temperatures Extremophile - prefers extreme temperatures Neutrophile - prefers moderate pH Halophile - prefers a highly salty environment Cyanobacteria - bacteria that uses oxygenic photosynthesis Rhizobium - genus of bacteria responsible for nitrogen fixation Identify and describe symbiotic relationships Any interaction between species that are associated with each other within a community is called symbiosis.  ○ Understand the types of symbiotic relationships and be able to identify/explain them if the relationship is described (mutualism, amensalism, commensalism, neutralism, parasitism) ○ Be able to describe an example of each Mutualism When both populations benefit from each other. Example: bacteroides thetaiotaomicron is a bacterium that lives in the intestinal tract. It digests complex polysaccharides plant materials that human digestive enzymes cannot break down, converting them into monosaccharides that can be easily absorbed by human cells. Amensalism When one population is harmed while the other is unaffected. Example: some amnesalist species produce bacterial substances that kill other species of bacteria. Commensalism When one population benefits while the other is unaffected. Example: the bacterium Stapphylococcus epidermidis uses dead cells of the human skin as nutrients. Neutralism When neither populations are unaffected by each other. Example: the coexistence of metabolically active (vegetative) bacteria and endospores (dormant,metabolically passive bacteria) Parasitism When one population benefits from harming the other. Examples: tetanus, diphtheria, tuberculosis, leprosy and pertussis. Compare normal/commensal/resident microbiota to transient microbiota  ○ Understand microbiomes* of common environments (e.g., human, soil, water) are different for various reasons, typically driven by environmental conditions and may change over time Microbiome refers to all prokaryotic and eukaryotic microorganisms and their genetic material that are associated with a certain organism or environment. The resident microbiota consists of microorganisms that constantly live on our bodies. Transient microbiota refers to microorganisms that are only temporarily found in the human body, and these may include pathogenic microorganisms. Hygiene and diet can alter both the resident and transient microbiota. The resident microbiota are amazingly diverse. They are important for human health because they occupy niches that might be otherwise taken by pathogenic organisms. Explain how prokaryotes are classified The nucleotide sequences in genes? By Stating patterns Gram- Positive and Gram-negative Section 4.2 Proteobacteria Describe the unique features of each class within the phylum Proteobacteria: ○ Alphaproteobacteria – general appreciation only*, but DO understand that this class includes obligate intracellular bacteria that require part of their life cycle to occur inside other cells called host cells (review the example provided and understand WHY they are called obligate intracellular pathogens) Alphaproteobacteria Capable of living in low-nutrient environment (Oligotroph) Obligate intracellular pathogens: require part of life cycle to occur inside host ○ Metabolically inactive outside host cells ○ Cannot produce own ATP so rely on cells or their energy needs  Ex. Rickettsia spp., R. prowazkii., C. trachomatis( cause trachoma*eye disease* and can lead to blind) ○ Betaproteobacteria – general appreciation only* It is a diverse group of bacteria. They can survive in a range of environments. ○ Gammaproteobacteria – general appreciation only*, EXCEPT for enteric bacteria (Enterobacteriaceae); understand the unique characteristics of this class of bacteria The most diverse class of gram-negative bacteria is Gammaproteobacteria, and it includes a number of human pathogens. Enterobacteriaceae is a large family of enteric (intestinal) bacteria. They are facultative anaerobes and are able to ferment carbohydrates. Within this family there are 2 distinct categories. The first category is called the coliforms, after its prototypical bacterium E. coli. Coliforms are able to ferment lactose completely. The second category, non coliforms, either cannot ferment lactose or can ferment lactose incompletely. ○ Deltaproteobacteria – general appreciation only*, EXCEPT that this is a small class of very diverse bacteria (SRBs, parasites, soil bacterium) It is a small class of gram-negative proteobacteria that includes 1. Sulfate-reducing bacteria (SRB) a. SRB uses sulfate as the final electron acceptor in electron transport chain 2. Bdelloviobrio - parasite of other gram-negative bacteria a. Invade then put themselves between plasma and cell wall, feed on host’s protein & polysaccharides 3. Myxobacteria - live in soil scavenging inorganic compounds a. Motile & high social(involved in lots of other bacteria group ○ Epsilonproteobacteria – general appreciation only*, EXCEPT that this is the smallest class and they are microaerophilic bacteria Gram-Negative bacteria that required really less oxygen (ALE)Give an example of a bacterium in each class of Proteobacteria Section 4.3 Nonproteobacteria Gram-negative bacteria and phototrophic bacteria Describe GENERAL features of gram-negative bacteria and how we differentiate them from gram-positive bacteria Comparison Between Gram-Negative and Gram-Positive Bacteria: Feature Gram-Negative Gram-Positive Bacteria Bacteria Peptidoglycan Thin Thick Layer Outer Present Absent Membrane Lipopolysaccha Present (in outer Absent rides (LPS) membrane) Gram Stain Pink or red (due to Purple (retains crystal counterstain) violet stain) Periplasmic Present Absent or very small Space Teichoic Acids Absent Present  Resistance to Higher due to Lower, more susceptible to Antibiotics outer membrane cell wall-targeting antibiotics Flagella May have External flagella, no periplasmic or periplasmic space external flagella Toxins Endotoxins (LPS) Exotoxins Examples of E. coli, Neisseria, Staphylococcus, Pathogens Pseudomonas Streptococcus, Bacillus Describe the unique features of nonproteobacteria gram-negative bacteria ○ general appreciation only*, EXCEPT to understand the unique characteristics of spirochetes and CRB group Spirochetes They are characterized by their long spiral shaped bodies (up to 250 micrometers). They are also very thin which makes it difficult for them to be viewed under a conventional brightfield microscope. - They are difficult to culture - Highly motile, use their axial filament to propel themselves CFB group (cytophaga, fusobacterium, and bacteroides) - They are rod shaped bacteria adapted to anaerobic environments, such as the tissues of the gums, gut. - They are avid fermenters, able to process cellulose in rumen, thus enabling ruminant animals to obtain carbon and energy from grazing. - Cytophaga are motile aquatic bacteria that glide. - Fusobacteria inhabit the human mouth and may cause severe infectious diseases. - Bacteroides make up 30% of the entire gut microbiome. Most of them are mutualistic. (ALE)Give an example of a nonproteobacteria bacterium in each category Describe the unique features of phototrophic bacteria ○ Understand the types of bacterial groups (e.g., purple sulfur, green sulfur, etc) and the unique characteristics, specifically if they are oxygenic or anoxygenic, strict anaerobes/facultative/etc, if they oxidize hydrogen sulfide, and their carbon source (i.e., CO2, organic). Sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria uses organic substrates, such as succinate and malate, as donors of electrons. Bacteria that use sunlight as their primary source of energy Purple sulfur bacteria - Oxidizes hydrogen sulfide into elemental sulfur and sulfuric acid. - Get their purple color from the pigments bacteriochlorophylls and carotenoids. - Chromatium are strict anaerobes and live in water. They use co2 as their only carbon source - Anoxygenic(did not produce oxygen as byproduct) Green sulfur bacteria - Anoxygenic - Use sulfide for oxidation and produce ;large amounts of green bacteriochlorophyll. - Chlorobium is a green sulfur bacterium that produces methane, a greenhouse gas. - Bacteriochlorophyll is stored in special vesicle-like organelles called chlorosomes. Purple nonsulfur bacteria - Anoxygenic - Uses hydrogen sulfide for oxidation. - Rhodospirillum are facultative anaerobes, which are usually pink rather than purple, and can fix nitrogen. - Potential ability to produce biological plastic and hydrogen fuel. - Facultative anaerobes Green nonsulfur bacteria - Use substrates other than sulfides for oxidation. Non-sulfide - Anoxygenic, using organic sulfites or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available. Cyanobacteria - Oxygenic photosynthesis, producing megatons of gaseous oxygen. - Amazingly adaptable, can thrive in many habitats including marine, freshwater, soil and even rocks. - They can live in a wide range of temperatures. - Can live as unicellular or in colonies. - Can be filamentous, forming sheaths or biofilms. - Many of them fix nitrogen. - Use chlorophyll a. - Some are harmful Identify phototrophic bacteria ○ If I provide you a picture of a soil/water column, depending on the environment (deep below the surface or floating at the top) you should be able to tell me which bacterium is growing where based on their unique characteristics * Section 4.4 Gram-positive bacteria Describe GENERAL features of gram-positive bacteria and how we differentiate them from gram-negative bacteria & what does it mean when we say these bacteria have high/low G+C content - Prokaryotes are identified as gram-positive if they have multiple layer matrices of peptidoglycan forming the cell wall. - Low G+C gram positive bacteria have less than 50% guanine and cytosine nucleotides in their dna. - High G+C gram positive bacteria have more than 50% guanine and cytosine nucleotides in their DNA. Describe the unique features of each category of high G+C and low G+C gram-positive bacteria  ○ High G+C, gram-positive (Actinobacteria* ): generally understand IF there are common unique characteristics across Genus, and where these microbes can be found (e.g., soil, human) - Most actinobacteria live in the soil, some are aquatic. - Vast majority are aerobic - Presence of several different peptidoglycans in the cell wall. ○ Low G+C, gram-positive*: generally understand IF there are common unique characteristics across Genus, and where these microbes can be found (e.g., soil, human) - A number of bacteria that are pathogenic. (ALE)Identify similarities and differences between high G+C and low G+C bacterial groups (ALE)Give an example of a bacterium of high G+C and low G+C group commonly associated with each category Section 4.5 Deeply branching bacteria Describe the unique features of deeply branching bacteria ○ Understand & recognize the Phylogenetic tree of life and be able to evaluate/compare the three main branches (Bacteria, Archae, Eukarya) The phylogenetic tree of life is a diagram that represents the evolutionary relationships between all living organisms on Earth. It shows how species have diverged from a common ancestor over time, with branches representing lineages. The three main branches of the tree of life are Bacteria, Archaea, and Eukarya, representing the major domains of life. 1. Bacteria Structure: Bacteria are prokaryotes, meaning they lack a nucleus and other membrane-bound organelles. Cell Wall: Most bacteria have a cell wall made of peptidoglycan, a unique molecule that provides structural support. Metabolism: Bacteria exhibit vast metabolic diversity, including photosynthesis (like cyanobacteria), nitrogen fixation, and aerobic/anaerobic respiration. Reproduction: Bacteria reproduce through binary fission, a simple form of asexual reproduction. Genetic Material: DNA is located in a single, circular chromosome, and they often have additional DNA in small rings called plasmids. Examples: Escherichia coli (E. coli), Staphylococcus aureus, Cyanobacteria. 2. Archaea Structure: Like bacteria, archaea are also prokaryotes, but they are genetically and biochemically distinct. Cell Wall: Unlike bacteria, archaea do not have peptidoglycan in their cell walls; instead, they have unique cell wall components, such as pseudopeptidoglycan or S-layer proteins. Environment: Many archaea are extremophiles, living in harsh environments such as high-temperature hydrothermal vents, acidic springs, or high-salt environments. Metabolism: Archaea have unique metabolic pathways, such as methanogenesis (producing methane), and can survive in anaerobic environments. Reproduction: They also reproduce by binary fission, budding, or fragmentation. Examples: Methanogens (methane producers), Halophiles (salt lovers), Thermophiles (heat lovers). 3. Eukarya Structure: Eukaryotes have complex, membrane-bound organelles, including a nucleus that encloses their DNA. Cell Types: Eukarya include both single-celled organisms (like protists) and multicellular organisms (like plants, fungi, and animals). Cell Wall: In eukaryotes, cell walls (if present) vary in composition. For example, plants have cell walls made of cellulose, and fungi have cell walls made of chitin. Metabolism: Eukaryotes exhibit a wide range of metabolic strategies, including aerobic respiration and photosynthesis. Reproduction: Eukaryotes reproduce both sexually (through meiosis) and asexually (through mitosis). Organelles: They possess specialized organelles like mitochondria (for energy production) and, in photosynthetic organisms, chloroplasts. Examples: Humans, plants, fungi, algae, amoebas. ○ Understand the concept of ‘last universal common ancestor’ (LUCA)  The Last Universal Common Ancestor (LUCA) refers to the most recent common ancestor of all current life forms on Earth. It represents the organism or group of organisms from which all existing species—bacteria, archaea, and eukaryotes—descended. LUCA is not thought of as a single individual, but rather as a population of organisms that shared certain core genetic and biochemical traits. ○ Understand the conditions that the deeply branching bacteria are adapted to live (harsh conditions=what are these conditions, where are these environments) - Deeply branching bacteria that still exist, were thermophiles or hyperthermophiles, meaning that they thrived at high temperatures. - Lived in hot springs, near underwater volcanoes and thermal ocean vents. - Also are resistant to uv light and ionizing radiation. - Conditions thought to dominate the earth when life first appeared. Give examples of significant deeply branching bacteria* ○ Recognize a deeply branching bacterium in a question when environmental conditions are provided (i.e., extreme/harsh conditions) Aquifex are hyperthermophiles, living in hot springs at temperatures higher than 90 degree celsius. Section 4.6 Archaea Describe the unique features of each category of Archaea - Archeal cell membrane is composed of ether linkages with branched isoprene chains. - Their cells walls lack peptidoglycan, but some contain a similar substance pseudopeptidoglycan. - The genomes of archaea are larger and more complex than bacteria. - Many are extremophiles. - No known pathogens. Explain why archaea might not be associated with human microbiomes or pathology - Archaea’s are usually found in extreme environments, which are not found in human bodies.  - They have unique cell structures that make them less detectable by the immune system.? Give common examples of archaea* commonly associated with unique environmental habitats ○ general appreciation only*, EXCEPT to understand the types of environmental habitats they are found - Crenarchaeota is a class of archaea that are all aquatic organisms. Most of them are hyperthermophiles and are able to grow at temperatures up to 113 degree celsius. - Methanogens have been found in hot springs as well as deep under ice in greenland. - Halobacteria require a very high concentration of sodium chloride in their aquatic environment. General notes: I will not be testing your ability to determine which microbe is causing an infection/disease based on symptoms. Although this may be helpful information if you’re pursuing a medical/nursing degree, you will not be tested on this here. I also will not provide you a picture of a microscope slide or other graphic and expect you to identify the Genus spp. If the OpexStax LO is greyed-out+strikethrough, then it will NOT be on any Exam ALE – If you see this, then this is covered in an active-learning exercise and will not be evaluated on an exam (*) - means do NOT memorize Genus or morphology (typically provided in a table); however, knowing some unique characteristics (common across many) would be helpful but not for every Genus Blue italicized text – The learning objectives with this formatted sub-bullet are gently covered in this course. The Blue italicized text formatted sub-bullet provides clarity as to the part(s) of the learning objective that is(are) applicable to this course. Red italicized text – these learning objectives were not explicitly stated in the textbook, but are implied in many others; for clarity, I added them so there was no confusion. Chapter 5: Eukaryotes of Microbiology Section 5.1 Unicellular Eukaryotic Parasites Summarize the general characteristics of unicellular eukaryotic parasites O Describe the role of the cyst and trophozoite stages in the Giardia life cycle (refer to the slides we review IN CLASS) Describe the general life cycles and modes of reproduction in unicellular eukaryotic parasites O Describe the role of the cyst and trophozoite stages in the Giardia life cycle (refer to the slides we review IN CLASS) - Only transmitted in cystic stage, trophozoite stage could not survive outside cell to be transmitted O Recognize (do NOT memorize) there are different life cycles (sexual/asexual) that eukaryotes follow to reproduce.*NOTE: The figures presented in this section (Fig. 5.4, 5.10, 5.11, 5.18) are some examples that help illustrate the complexity of this process. Identify challenges associated with classifying unicellular eukaryotes Explain the taxonomic scheme used for unicellular eukaryotes (*do NOT memorize the eukaryotic supergroups or the examples in the figure 5.8 table) Give examples of infections caused by unicellular eukaryotes O Name two eukaryotic pathogens and the diseases they cause (look at the slides presented in class for this) - Giardia (giardiasis), malaria (malaria), algal bloom (algae) Section 5.2 Parasitic Helminths (not covered in this class) Section 5.3 Fungi Explain why the study of fungi such as yeast and molds is within the discipline of microbiology - their spores are microscopic OBriefly explain what mycoses are. - clusters of fungi Describe the unique characteristics of fungi O Describe what hyphae are (don’t memorize the specific forms in Figure 5.25) - branches of fungi Section 5.4 Algae Explain why algae are included within the discipline of microbiology O Explain the ecological and environmental importance of algae Describe the unique characteristics of algae They are important because they are responsible for the production of 70% of the oxygen and organic matter in aquatic environments. - Algae are autotrophic protists that can be unicellular or multicellular. - Algal cells can have one or more chloroplasts that contain structures called pyrenoids to synthesize and store starch. - O Provide the major source of energy for most algae The major source of energy for most algae is sunlight. O Describe products used in laboratories that are derived from algae Identify examples of toxin-producing algae* (do not memorize specific genus or species) Algae are the source for agar, agarose, and carrageenan, solidifying agents used in laboratories and in food production. Red aglae O Describe the major features of dinoflagellates - They are mostly marine organisms and are an important component of plankton. - They may be heterotrophic, phototrophic, and mixotrophic. - The photosynthetic ones use chlorophyll a, chlorophyll c2. - They generally have 2 flagella, causing them to whirl. - Some of them have a cellulose layer that forms a hard outer shell, called the theca. - They produce neurotoxins that can paralyze fish and humans. O Explain why poisoning of shellfish occurs during red tides The major toxins produced are Gonyaulax and Alexandrium both which cause paralytic shellfish poisoning. Compare the major groups of algae in this chapter, and give examples of each Golden algae (Chrysophyta) Brown algae (Phaeophyta) Diatoms (bacillariophyto) Green algae Red algae Classify algal organisms according to major groups Section 5.5 Lichens Explain why lichens are included in the study of microbiology - They are made up of one-part cyanobacteria/green algae and one-part fungi and those components are microscopic. Describe the unique characteristics of a lichen and the role of each partner in the symbiotic relationship of a lichen O Describe the role of each organism in this symbiotic relationship and what each “gets out” of it (or loses because of it) algae/cyanobacteria gains ability to live anywhere, fungi gain ability to capture energy from light (photosynthesis) O Explain why most scientists consider the relationship of these organisms to be a controlled parasitism The cyanobacteria/algae do not need to live anywhere and could thrive better without the fungi in an environment better suited to them. O*Do not memorize parts of the lichen in Figure 5.38 Describe ways in which lichens are beneficial to the environment O Briefly describe why lichens are important for most terrestrial ecosystems Lichens perform photosynthesis anywhere, which produces O2 Chapter 6: Acellular Pathogens NOTE: An acellular pathogen that ONLY infects prokaryotes is called a bacteriophage (aka “phage”), while an acellular pathogen that infects eukaryotes is called virus (e.g., plant virus or animal virus). CAUTION: This Chapter will be revisited for all mid-term Exams; only certain sections and concepts will be covered for each mid-term Exam, but the Final Exam will evaluate your cumulative understanding of the concepts presented in this Chapter. Please refer to the class lecture materials when determining which LO’s are applicable to EACH exam; a general break-out by mid-term Exam has been suggested below, but this is subject to change. Section 6.1: Viruses [Exam 1, 2, 3 + cumulative] Describe the general characteristics of viruses as pathogens Describe viral genomes ○ Common pathogenic viruses Table 6.2 provides a good list of genomes found/present in the more popularized eukaryotic viruses; you should understand the common types of virus genomes. You do NOT need to memorize the Family or Example Virus or clinical features noted in this table. Describe the general characteristics of viral life cycles Differentiate among bacteriophages, plant viruses, and animal viruses Describe the characteristics used to identify viruses as obligate intracellular parasites Section 6.2: The viral lifecycle [Exam 2 & 3 + cumulative] Describe the lytic and lysogenic life cycles Describe the replication process of animal viruses Describe unique characteristics of retroviruses and latent viruses Discuss human viruses and their virus-host cell interactions Explain the process of transduction Describe the replication process of plant viruses Section 6.3: Isolation, culture, and identification of viruses [Exam 1, 3 + cumulative] Discuss why viruses were originally described as filterable agents Viruses were originally described as filterable agents because of early experiments in which infectious agents passed through filters that were designed to trap bacteria. At the time, scientists did not know that viruses existed, and these filters were used with the assumption that bacteria were the smallest pathogens. The discovery of viruses came about when certain infectious materials were found to retain their ability to cause disease, even after filtration. Here's the background and significance. Describe the cultivation of viruses and specimen collection and handling Compare in vivo and in vitro techniques used to cultivate viruses Section 6.4: Viroids, virusoids, and prions [Exam 1] Describe viroids and their unique characteristics - They consist only of a short strand of circular RNA capable of self-replication. - Do not have a protein coat to protect their genetic information. - Can result in devastating losses of commercially important agricultural food crops grown in fields and orchards. Describe virusoids and their unique characteristics - Subviral particles best described as non-self-replicating ssRNAs. - Unlike viroids, virusoids require that the cell be infected with a specific “helper” virus. - The virusoid genomes are small , only 220 to 338 nucleotides long. A virusoid genome does not code for any proteins but instead serves only to replicate virusoid RNA.  Describe prions and their unique characteristics - Do not have a rna/dna. - A prion is a misfolded rogue form of a normal protein. - It could be caused by a genetic mutation or occurs spontaneously. Can be infections and cause other proteins to be misfolded forming plaques. - Known to cause various forms of transmissible spongiform encephalopathy. A rare degenerative disorder that affects the brain and nervous system. General notes: I will not be testing your ability to recall OR determine which microbe is causing an infection/disease based on symptoms. Although this may be helpful information if you’re pursuing a medical/nursing degree, you will not be tested on this here. I also will not provide you a picture of a microscope slide or other graphic and expect you to identify the Genus spp. of an organism. If the OpexStax LO is greyed-out+strikethrough, then it will NOT be on ANY exam ALE – If you see this, then this is covered in an active-learning exercise and will not be evaluated on an exam (*) - means do NOT memorize Genus or morphology (typically provided in a table); however, knowing some unique characteristics (common across many) would be helpful but not for every Genus Blue italicized text – The learning objectives with this formatted sub-bullet are gently covered in this course. The Blue italicized text formatted sub-bullet provides clarity as to the part(s) of the learning objective that is(are) applicable to this course. Red italicized text – these learning objectives were not explicitly stated in the textbook, but are implied in many others; for clarity, I added them so there was no confusion.