M200 Microbiology Exam 1 Notes
M200 Microbiology Exam 1 Notes BIOL-M200
Popular in Microbiology with Diseases by Body System
Popular in Microbiology
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This 15 page Study Guide was uploaded by Sarah Rebey on Friday March 25, 2016. The Study Guide belongs to BIOL-M200 at Indiana University taught by Cheng Kao in Spring 2016. Since its upload, it has received 25 views. For similar materials see Microbiology with Diseases by Body System in Microbiology at Indiana University.
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Date Created: 03/25/16
STUDY GUIDE, EXAM 1 I. General introduction and the history of microbiology This section is intended to introduce you to microbiology and to, hopefully, make you interested in microbes. It is also important to appreciate the historical advances we have made in microbiology that have shaped our world. Please define “microbiology”. The study of organisms we cannot see with the human eye. Bacteria, bacteria, protists, fungi. What common foods are made using microbes? Sour cream, yogurt, cheese, chocolate, soy sauce, bread, beer, wine. Which of our organs contain high amounts of microbes? Intestines and skin Many microbes are part of our normal microbiome. What do these microbes produce for us to allow us to live? Digest foods and produce vitamins. Produce most of the oxygen and fix most of the nitrogen. Please name two other ways in which microbes help us stay healthy? Prevent the growth of pathogenic bacteria. Regulate our body’s normal functions. Can it be argued that we have microbes in just about every cell of our body? Yes. What is the evidence for the descendants of microbes living in our cells? Bacteria were the ancestors of our organelles- mitochondria Mitochondria has its own genome. The CDC has stated that Clostridium difficile as causing 250,000 infections a year. What medical treatments typically precede C. diff infection? Hospitalized patients or nursing home patients are more likely to develop it. Example of a medical treatment preceding it would be a insertion or reversal of a colostomy bag. What are the symptoms for C. diff infection? Abdominal discomfort, weight loss, watery diarrhea What structures formed by C. diff make them more difficult to kill? Endospores and resistance to antibiotics. 1 What are typical treatments for C. diff? Antibiotics: metronidazole and vancomycin. Although the vast majority of microbes either leave us alone or are beneficial, some do cause diseases. A section below will summarize the diseases caused by microbes. Which are the following are prokaryotic? Which are eukaryotic? Bacteria, Archaea, Protists, Algae, Fungi, Viruses Prokaryotes: bacteria & archaea Eukaryotes: protists, algae, fungi Neither: Viruses The three major domains of life were derived from the sequences of ribosomal RNAs. What are the names of the three domains? Bacteria, Archaea, and Eucarya (BAE) What is ribosomal RNA? Make up 60% of ribosomes and used for protein synthesis. Other 40% is protein. Our beloved Earth was formed approximately 4.5 billion years ago. Using radiometric dating, bacteria have been present on earth for at least three billion years. What is radiometric dating? Dating by using the isotopes By looking at the decay of byproducts. What is a stromatolite? Layers of bacteria over billions of years that changed the physical condition of the ocean. Of the three domains of life, which likely produced the oxygen on earth ca. 2.5 billion years ago? Bacteria Before the scientific method was used, there is a widespread belief that health is due to the balance of the four humors. What are the humors and what was a common treatment for people who had an imbalanced of humors? The four humors were yellow bile, black bile, blood and phlegm. The common treatment would be to ‘balance’ the humors by draining one of them out of the body i.e. blood to put the humors back into balance. Blood-letting 2 What is the “the scientific method”? Why is it important to use the scientific method? Who used the scientific method to identify the organism that produced wine? The scientific method is a framework for scientific research It is important to use the scientific method to determine if a hypothesis is true and implement it as theory or law. Louis Pasteur used the scientific method to identify the organism that produced wine. What is a hypothesis? How did Louis Pasteur test the hypothesis that bacteria are responsible for fermenting grape juice to produce alcohol? A hypothesis is an idea or explanation for something that you can test. Pasteur tested the hypothesis for fermentation by using 4 flasks with different treatments. Flask 1- sealed flask with no microbes Flask 2- curved neck, also free of microbes Flask 3- sealed flask inoculated with bacteria. Flask 4- sealed flask inoculated with year. *this produced wine = fermentation Describe what is done during pasteurization? How did pasteurization improve people’s health? Pasteurization is heating liquids to a high temperature for a short time in order to kill most bacteria and increase shelf life of foods. It improved people’s health by allowing foods that could cause food- borne illness to not go bad as quickly and kill the bacteria that caused the illnesses. It took a long time for Germ Theory of Disease to replace the idea that disease is caused by an imbalance of humors, or bad air (miasma). What factors prevented some, even highly educated individuals to not believe the Germ Theory of Disease? Some people believed that doctors couldn’t be responsible for making patients sick. The Koch’s Postulates have been influential in establishing the causative agents for diseases in medical microbiology. What are the four Koch’s postulates and how which of them can be difficult to fulfill? 1. The microbe must be found in abundance in all diseased organisms but not in healthy organisms. 3 2. The microbe must be isolated from a diseased organism & grown in a pure culture. 3. The culture microbe should cause disease in a healthy organism (This is the most difficult one to fulfill because it is unethical to infect humans with a disease for research) 4. The microbe must be reisolated from the inoculated, diseased host & identified to be the same as the introduced microbe. II. Chemistry, including biological chemicals Chemistry provides the underlying basis for understanding life on earth. Chemistry can also form the basis to provide solutions to problems that we need to solve. In this section, we reviewed basic chemistry (atoms, elements, bonding, chemical reactivity) and then the macromolecules that are the components for microbes. The same macromolecules are also essential parts of us. A chemical that is very useful in a healthcare setting and in our homes is bleach, Sodium hypochlorite. The chemical formula for bleach is NaClO. If you had a periodic table, can you determine the atomic weight for bleach? Na-O-Cl Atomic weight = sum of masses of protons, neutrons, and electrons the atomic numbers for the elements in bleach? Atomic number= the number of protons in the nucleus the type of chemical bond that is formed in bleach. Types of bonds: Covalent: formed by two atoms that share electrons Nonpolar covalent bonds: electrons shared equally by two atoms Polar covalent bonds: electrons unequally shared Ionic bonds: attraction between atoms, but no sharing of electrons. Can form salts H bonds: a type of ionic bond that involves hydrogens bonded to Oxygen or nitrogen Weak forces: attractive or repulsive forces between molecules. Sodium forms ionic bonds and Chlorine is covalent bond. Is bleach a molecule? Is it a compound? No it is a compound (a molecule composed of more than one element) 4 What happens to bleach when it is dissolved in water? Based on the periodic table, which parts of the dissolved bleach is more electronegative and, hence, more likely to react. It breaks into Na+ and –OCl (hypochlorite) Based on EN, the hypochlorite would be more likely to react. What will bleach react with in microbes to help us inactivate them? Dissolve lipids, break fatty acids, and interact with molecules including amino acids. What are the elements that are common to life? Will you be able to identify the elements in a molecule, say ATP? CHOPKNS Ca Fe Mg Na Cl Elements of molecule ATP (adenosine triphosphate) Three phosphate How is an isotope different than the standard elements in the periodic table? An isotope has an a different number of neutrons in the nuclei than its atomic number. Isotopes have many uses in medicine. Please name some uses. Would you use a stable isotope or an unstable one? In medical procedures, do we tend to use isotopes with long half-life (takes a long time to decay to a non- isotope form) or a short one? Why? -Sterilization of medical equipment, diagnosis through examination with PET scans, and therapy through relieving pain or killing cancer cells. -Use stable isotopes because unstable ones release radioactive decay? -We want a short half life so it does not remain in our bodies for long. What are the four major classes of macromolecules in living organisms? Where are they located in a bacterium, in a virus? We did not go through the locations of the macromolecules in a eukaryotic cell, but you should be able to do so. Four Classes: Carbohydrates, lipids, nucleic acids, and proteins Bacteria: o Capsule- Carbohydrates o Cell Wall- carbs, proteins o Cytoplasmic membrane- proteins, lipids o Ribosomes- proteins, nucleic acids o Cytoplasm- lipids, carbs, nucleic acids, proteins o Nucleoid- nucleic acids, proteins o Flagella- proteins Viruses: 5 o Enveloped virus (flu, ebola) RNA- nucleic acids, proteins Capsid- lipids, proteins, carbs? Hemaggluthin- proteins Neuraminidase- proteins o Nonenveloped virus (polio) (bacteriophage) DNA- nucleic acids Head- proteins Internal proteins- proteins Tail sheath- proteins Neck- proteins End plate, pins, etc – proteins NO LIPIDS Eukaryotes: Look up in book. What are carbohydrates? How do carbohydrates function in a bacterium? Name two structures in a bacterial cell that contain carbohydrates. What are the subunits in a carbohydrate? Will these subunits interact with water in an aqueous environment? “Hydrated carbons” that form sugars. Stabilize the cell from the environment Increase invasiveness Help escape immune cells Cell wall- sugars + amino acids Carbs function in a bacterium by: Two structures in a cell that contain carbs are: cell wall and capsule Subunits: Yes these subunits interact with water in an aqueous environment? Cellular molecules should be considered in the context of water. If you have two molecules, one that is polar and one that is not, which will be better able to interact with water? The polar molecule. Water is polar, and like attracts like (hydrophilic) What is a phospholipid, which parts of it can interact with water and which cannot? Phospholipids consist of a glycerol molecule, two fatty acids, and a phosphate group that is modified by an alcohol. The phosphate group is the negatively-charged polar head, which is hydrophilic. The fatty acid chains are the uncharged, nonpolar tails, which are hydrophobic. 6 Will a membrane that contains more unsaturated lipids be more or less fluid than one that contains less saturated lipids? The more unsaturated lipids, the more fluid the membrane. When it is unsaturated, there are kinks in the C=C bond that do not allow it to compact as easily, and therefore remain in a liquid state. What are proteins? How do they serve functions in a bacterium? What structures in a bacterium that will contain proteins? Proteins are amino acids linked together by peptide bonds. They form structures, signaling molecules, and enzymes in the body. In bacterium, they form the inside cell and outside of the cell, and help interact with other molecules. Also, the enzymes they create help catalyze reactions. Structures with protein are the cell wall, membrane, cytoplasm, and nucleoid. Proteins are made of amino acids linked together by peptide bonds. The amino acid sequence contributes to the folding and the functional properties of proteins. How do these subunits contribute to protein structure and function? Which of the four general groups of amino acids can interact with water in an aqueous environment? Which class of amino acids is more likely to interact with the lipids in a membrane? Can you predict the class of subunits that can interact with cholesterol? Hydrophobic The ribosome is an amazing machine that synthesizes proteins. Please describe the components of the ribosome and their function. What is the source of the information that will direct protein synthesis. What are nucleic acids? How do they serve functions in a bacterium? Are the nucleic acids located within a bacterium? What are the subunits in a nucleic acid and what are the parts in the subunit? How do these subunits contribute to nucleic structure and function? What are the distinguishing features of DNA from RNA? How is a nucleoid different than the chromosomes in our cells? What is a plasmid? What are differences in the function of DNA versus RNA? Why is H-bonding in nucleic acid important in the function of the nucleic acids? III. Cellular structures Cellular structures in bacteria are important for how they live. They are also important for us to diagnose and classify bacteria. Many also have amazing properties that we can learn from and perhaps use in developing new technologies. The structures are also made of the macromolecules and thus, 7 allow me to build from our analyses of macromolecules. Importantly, you should now see that the structures represent many variations in common themes. For example, there are different ways for bacteria to use flagella to move in a medium. Knowing that there are these variations will allow you to think more about new microbes that we will encounter. The structures in a microbe are often adapted to serve the needs of a living organism. What are the four basic properties of living organisms? Growth Reproduction Responsiveness Metabolism Like our cells, bacterial cells can sense the environment and then respond. The sensing/response can be regulated in complex ways and result in the change in cell structures, metabolism and the production and/or degradation of cellular molecules. In response to the environment the bacterium can move toward or away from a chemical (chemotaxis). The cells could also move toward or away from light (phototaxis), oxygen, etc. Flagella are commonly used by a bacterium to move in motions described as runs and tumbles. What is a run versus a tumble? Runs- counterclockwise flagellar rotation produces movements of a cell in one direction for some time (positive stimuli) Tumble – abrupt, random changes in direction. Tumbles results form clockwise flagellar rotation where each flagellum rotates independently. (negative stimuli) Both occur in response to a stimuli Can you draw a flagellum and generally describe the function of each of the parts of the flagellum? Filament: a long hollow shaft, that extends out into the cell’s environment and is composed of many identical globular molecules of protein called flagellin. Hook: At the base, where the filament inserts and is made of different proteins. Basal body: composed of different proteins, anchors the filament and hook to the cell wall and cytoplasmic membrane by means of a rod and a series of either two or four rings of integral proteins. How do polar flagella differ from peritrichous flagella? How does an axial filament differ from flagella? 8 Peritrichous flagella cover the surface of the cell. Polar flagella are only at the ends. Axial filament differs from flagella because they are made up of endoflagella which wrap around the cell between the cytoplasmic membrane and an outer membrane (instead of extending into the environment around them) Fimbriae and pili are made of related proteins and have overlapping functions. What are the properties and functions of a fimbriae or a pilus? Why is a conjugation pilus potentially important in the spread of antibiotic resistance? Fimbriae: shorter than a flagella, and they are sticky, bristlelike projections that adhere to each other and other substances. Hundreds per cell. Used for movement, and contain enzymes that can render soluble toxic metal ions into a nontoxic form. also form Biofilms: slimy masses of microbes made up of fimbriae and glycocalyces. Pilus: a special type of fimbriae, which are longer but still shorter than flagella as well. There are only a few per cell, and they transfer DNA from one cell to another via conjugation. I’d assume pilus are important in the spread of antiobiotic resistance because they can pass along the DNA information of resistant bacteria to other cells in order for them to survive. Uropathogenic E. coli have specialized proteins at the end of their fimbriae. What are these proteins and how do they contribute to pathogenesis? They adhesins attached to fimbriae that help them attach to the urinary tract. The bacterial cell wall has many functions. Please list these. To inhibit bacteria, we have developed antibiotics such as penicillin to inhibit cell wall synthesis. What will happen to the bacterium if cell wall synthesis was inhibited? Bacteria are broadly categorized as Gram positive and Gram negative. Can you identify the differences in these two classes of bacteria? Gram positive: thick PG layer. Has poly alcohols Gram negative: thin layer PG layer. Has LPS The cell wall is primarily composed of Peptidoglycan (PG). What are the molecules in the glycan portion of PG and what is the peptide portion? Glycan= NAG and NAM molecules. Covalently linked in chain. 9 Peptide= peptide cross bridges that link NAG and NAM to each other. In addition to the PG, what other molecule can be associated with the Gram- positive bacterial cell wall? Poly alcohols. Mycolic acid The PG of a Gram-negative bacterium contains an outer membrane bilayer. Within this membrane are specialized polysaccharide-lipid molecules called lipopolysaccharides (LPS). The Lipid A portion of LPS is also called endotoxin. How can endotoxin affect us? Lipid A triggers an immune response? Please know the steps in the Gram staining procedure and how they affect the staining of the PG. 1. Stain with crystal violet – primary stain Gram + 2. A mordant (iodine) 3. A decolorizing agent (alcohol wash) 4. And a counterstain (Safranin) to color what is remaining Gram - Both the Gram-positive and Gram-negative bacteria have an inner membrane called the cytoplasmic membrane. How does this membrane regulate the passage of substances into and out of the cell? Are there specific molecules that regulate selective uptake of matter? Will membranes help to generate electrical potential across the cells? Endospores are amazing structures. Please describe the properties of endospores. Are endospores formed only by Gram-positive bacterium like Bacillus anthracis? When are endospores induced to form? Thick walled spores that form inside bacteria that are resistant to harsh conditions. Gram-positive mostly. Special procedures are needed to inactivate endospores of pathogens. Failure to do so may result in contaminated medical instruments and future infections. Please provide some ways that endospores could be inactivated. Bleach, high pressure, heat. Many bacteria contain inclusions within their cells. Some of these are storage granules that can be used when resources are scarce. What are examples of materials that are stored by bacteria? Minerals, carbs, polyphosphates, sulfur and iron. Also BT toxin to eat at insects intestines in cotton. IV. Products that we have derived from microbes. 10 The more we learn about living organisms, the more we can put the knowledge toward our use. For example, the properties of pathogenic microbes are used to design therapies and to modify our handling of them. One example is that knowledge that Streptococcus pyrogenes, the causative agent of Puerperal Fever, can contaminate skin of healthcare workers and be transmitted to patients. This knowledge has caused (albeit slowly) changes in medical practice. Our knowledge about microbes, along with a good dose of human ingenuity, allows many microbes and microbial molecules to work for us. An area of science derived from use of biological information, and biological matter, is called biotechnology. I have sprinkled these throughout the lectures, in places that fit with the materials, in order to show you how knowledge about microbes can be put into use. Throughout the first six lectures, several microbial products have been presented. Here is a summary. Smallpox vaccine- made from virus “vaccinia” which is a type of pox similar to smallpox but prevents the causation of the virus. Milkmaids were resistant from cowpox and therefore didn’t get smallpox. Wines- fermentation with yeast cells Recombinant insulin- used E. Coli to produce insulin instead of extraction from animals. Extracted the bacteria and purified it to produce more and cheaper insulin. (Also used yeast) Used to treat diabetes. Pasteurized foods- heated to high temperatures to kill the pathogens within them and stop food-borne illnesses Xanthan gum- a polysaccharide secreted by bacterium Xanthomonas campestris which is used as a food modifier to thicken and prevent ingredients from separating. CRISPR / Cas9 RNA-enzyme complex, isolated from a bacteria that allows us to change the genomes of eukaryotic cells. Bacillus thuringiensis (BT) toxin – gram-positive bacterium used as a biological pesticide by genetically modifying crops (such as cotton) so that it eats at the intestines of insects. Please briefly describe the organism (bacteria, virus, etc.) used to generate these products how the products are made and how they are used. V. Microbes that cause diseases. 11 Although the vast majority of microbes either leave us alone or are beneficial, some do cause diseases. Given that most of you have are interested in a profession in the medical area, we have presented several diseases in sections. Understanding these diseases can be a great way to organize concepts in microbiology and to put into place how structure and function of microbes can cause us harm. In addition, understanding the microbes that cause diseases should help you think of solutions, many of which are already in place in healthcare settings. In the list below, which are diseases caused by bacteria? Which can be diseases caused by viruses? Diptheria- bacteria Tuberculosis- bacteria Bubonic plaque- bacteria The common cold- virus Poliomyelitis- virus Cholera- bacteria The Flu- virus C. diff- bacteria Malaria- neither; caused by a protozoan AIDS- virus Puerperal fever- bacteria Urinary tract infection- bacteria Anthrax- bacteria; spore former Rabies- virus Smallpox- virus Atypical pneumonia caused by Mycoplasma pneumonia-bacteria Are any of the bacteria spore formers? C. Difficile Anthrax Which of the bacterial pathogens have peptidoglycan that confer the shape of cocci and which are rods? Strep= cocci Have we discussed any human diseases caused by Archaea? Why is this the case? No, there are no known pathogens known to archaea. 12 In-class exercises In these exercises, we are trying to get you to think about the information presented in lectures and also to discuss these with your classmates. I anticipate that the type of questions in these exercises will be some of the more challenging ones that you will encounter in Exam 1. I am pasting them for you to more fully consider them. Exercise 1. It is important to be able to distinguish Eukaryotes and Prokaryotes, as they have different properties, including sensitivity to certain treatments. Which of the following are prokaryotes? Please select the one best answer. A. Streptococcus epidermidis B. A mouse C. Protozoan D. Archaea E. A and D Exercise 2. Robert Koch’ postulates have helped scientists prevent the misdiagnosis of diseases. This is important. Let’s assume that you have identified, for the very first time, a virus that only infects people and causes severe immunodeficiency. You want to follow Koch’s postulates to prove that the virus causes the disease. However, which of the 4 postulates will be the most problematic to implement? A. 1 B. 2 C. 3 *unethical to infect humans D. 4 E. None of them 13 Exercise 3. Nitrogen has 5 electrons in its outer shell. Hydrogen has 1 electron in its outer shell. If you mix together elemental Nitrogen and Hydrogen, which of the following molecules will you form: A. Nitrogen that has three bonds to another nitrogen (N2). B. Hydrogen that is bonded to another Hydrogen (H2). C. Nitrogen bonded to 3 hydrogens (NH3) D. Nothing. E. The products in A, B and C, but in different ratios. Exercise 4. Horrors! You identified a new pathogenic bacteria that can lyse people’s Red Blood Cells (RBCs). When you examine the broken RBCs carefully, it appears that the Fatty Acid chains in the phospholipids of the RBCs are bound to a small peptide of two amino acids. You can’t wait to determine the amino acid sequence of the peptide so that you can start to design a therapy. Before the sequence is known, which of the 4 peptides below is most likely to bind to the long tails of the fatty acids? A. Lysine – Glutamate B. Threonine – Arginine C. Valine – Leucine D. Aspartate - Glycine Exercise 5. Which one of the following statements concerning a prokaryotic flagella is true? A. 2The basal body of the flagellum rotates to drive the rotation of the filament. B. The flagellum is attached to the cytoplasm of the cell. C. The Lyme disease bacterium has peritrichous flagella. D. The flagella of the bacterium can sense food and to trigger chemotaxis to food. Exercise 6. Although the vast majority of bacteria have cell walls, there are exceptions. One such bacterium belongs in the genus Mycoplasma. The species Mycoplasma pneumoniae is associated with an atypical pneumonia. Based on your knowledge on bacterial structures and their function, select the one answer that best describe Mycoplasma. A. Mycoplasma pneumoniae infection should be treated immediately with antibiotics such as penicillin. 14 B. Mycoplama likely use other molecules than peptidoglycan to reinforce their cellular membranes. C. Mycoplasmas likely do not have a free-living form; they are always associated with a host cell. D. Only B and C are true E. A, B, and C are all true. 15
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