Micro Exam 1 Study Guide
Micro Exam 1 Study Guide 3050
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Popular in Microbiology
This 15 page Study Guide was uploaded by Luke Holden on Friday February 5, 2016. The Study Guide belongs to 3050 at Clemson University taught by Dr. Rudolph in Winter 2016. Since its upload, it has received 72 views. For similar materials see General Microbiology in Microbiology at Clemson University.
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Date Created: 02/05/16
UNIT 1 STUDY GUIDE for LECTURE TOPICS MICR 3050 for Majors Spring 2016 OBJECTIVES (see note below): Chapter 1 1. Define “microorganism” and describe the types studied by microbiologists (cellular and acellular). a. Any acelluar or cellular entity too small to be seen with the naked eye. b. 3 Domain System i. BacteriaSingle celled, live in extreme environments, majority have a cell wall abundant in soil ii. Archea Distinguished by RRNA sequences 1. No peptidoglycan 2. Unique lipid membrane 3. Extreme environments with high salt and temperature 4. Thermophiles High Temp organisms 5. Halophiles high salt organisms iii. Eukarya 1. Protisitslarger than bacteria and archea a. AlgaePhotosynthetic and produce 75% of the earth’s oxygen b. Protozoa –unicellular and motile hunters and grazers of the micro world. They can also aid in the digestion of cellulose 2. Slime moldsThese guys aresthe two timers. They behave like protozoa during the 1 stage of life. But then, during the second stage they behave like fungi. During the first stage they ingest food particles whereas the second part of life they make their own. 3. Water moldsgrow on surface of freshwater and feed on the decaying vegetation such as logs and mulch. They are the cause of the great potato famine 4. Fungimolds and mushrooms a. These guys form thin threadlike structures called hyphae. They absorb nutrients from the environment and are the cause of bread to rise and some antibiotics c. Acellular i. Virus most invade a host cell and use its DNA ii. Viroids+satallites infectious RNA which is really bad on plants and is the cause of Hepatitis iii. Prions Infectious misfolded protein cause of Mad Cow iv. Whenever you see a big microorganism look to see if the organism has highly differentiated tissues. If it does, then it is NOT a microorganism. 2. Understand the importance of microorganisms (scope and relevance). a. 1/3 of Nobel Prizes awarded to microbiology b. Most populous and diverse group of organisms. c. Everywhere d. Huge recycling role e. 50% of carbon is in bacteria f. 90%Nitrogen is in bacteria g. Beneficial and are excellent tools for study 3. Compare and contrast prokaryotic and eukaryotic microbial cells. a. Prokaryotic No nucleus or membrane bound organelles. b. Eukaryotic Nucleus and membrane bound organelles. 4. Explain how the Universal Phylogenetic Tree was developed. a. Back in the ye old days where there was nothing around, there had to be something that could do all the work in expressing things in the cell. DNA can do nothing but store information and RNA is only good for expressing proteins, regardless, there had to be something that could replicate DNA and create proteins Ribozymes b. The universal phylogenetic tree is a bush like structure that has the three domains all originating form one common ancestor called the LUCA (Last Universal Common Ancestor). This tree is created using the RRNA subunits. As you increase the # of ribosomal differences=you increase the genetic difference. The tree does not measure time when the ancestor split… merely the differences between the two!!! 5. Distinguish between the three domains of life and explain their relatedness. a. Bacteria Single celled, live in extreme environments, majority have a cell wall abundant in soil b. Archea Distinguished by RRNA sequences i. No peptidoglycan ii. Unique lipid membrane iii. Extreme environments with high salt and temperature iv. Thermophiles High Temp organisms c. Eukyara Protisitslarger than bacteria and archea i. AlgaePhotosynthetic and produce 75% of the earth’s oxygen ii. Protozoa –unicellular and motile hunters and grazers of the micro world. They can also aid in the digestion of cellulose iii. Slime moldsThese guys are the two timers. They behave like protozoa during the 1 stage of life. But then, during the second stage they behave like fungi. During the first stage they ingest food particles whereas the second part of life they make their own. iv. Water moldsgrow on surface of freshwater and feed on the decaying vegetation such as logs and mulch. They are the cause of the great potato famine v. Fungimolds and mushrooms 1. These guys form thin threadlike structures called hyphae. They absorb nutrients from the environment and are the cause of bread to rise and some antibiotics 2. Halophiles high salt organisms 6. Be familiar with the current theories of microbial evolution and the evidence used to support these theories. a. Endosymbiotic Theory: This theory revolves around endosymbiosis which is the ability of what organism to live inside another. Since mitochondrion have their own set of DNA, it is reason to think that the first microbial cells lived inside the Mitochondrion. The products of metabolism leaves H2 and CO2 which is also the hydrogen hypothesis. This is how the first cells started. b. The microbes then underwent lots of mutation to create their genetic diversity and certain natural selected features. c. Then, HGT took over. i. 3 Types: 1. Transformation Uptake of Naked DNA 2. Conjugation This is the use of a sex pilus to directly contact another cell and transfer its genetic material. 3. Transduction This is when bacteriophages are released into the host cell and when the viral DNA gets tangled up with the bacterial DNA and is then replicated along with it. ii. The BIG point: HGT allowed genetic diversity to take place across the SAME generation. 7. Define the prokaryotic “species” and the bacterial strain. a. Collection of strains that share stable properties of each other yet differ greatly from other strains b. Strains: Single pure microbial culture i. When comparing strains, you need to chase a “type strain” This strain is the baseline for all of the other strains you will collect and will base your classification off of. This type strain however, may not always be the most represetnive, however, you must remain consistent in you r classification so you must keep the type strain as is. 8. Explain how microorganisms are named. a. Two part name i. Generic name (genus) (capitalized) ii. Epithet (not capitalized) iii. Example: Stapholoccus areus or S. areus. iv. Make sure to write out the full name and then abbreviate if using it in a paper 9. Know the contributions of the scientists discussed to the science of microbiology. a. Robert Hooke Described the fruiting structure of molds b. Antwan van Leuweenhooke The father of microbiology because he was the first to accurately describe bacteria c. Spontaneous Generation: This is where microbial organisms appear out of this air. d. Fransco Redi He disproved spontaneous generation for large animals such as flies: e. f. However, the supporters of spontaneous generation were still outraged sying that the reason that that experiment does not prove them wrong is because you need air to have spontaneous generaiton and that experinent did not allow air in. g. Louis Pastur HUGE he showed how to sterlize a solution, pasturization, vaccines, and other advances in microbiology. He settled the controversy by boiling a nutrient broth to get it sterrile and then placing it in a long neck flask where air could reach the solution but the dust could not. It should that the microbial growth occurred on the tip of the flask and not the broth which ment that spontaneous generation is flase. When he broke the long neck off, microbial growth occurred. h. i. John Tyndall proved that dust carried the microorganisms on the tip of Louis Pastur’s flask j. Ferdinan Cohn was bale to discover the endospore. He also classified bacterial organisms based on their shape and was able to use the term baccilllus for the first time. k. Jospeh Lister This was a small boy who had contracted rabbies at the time when louis pastur was working with rabbies and vaccines. His mother brought him to Pastur and asked if there was anything he could do. He had some rabbit rabbies bacterium that had been incubbating for a long period of time and he had had success on his animal subjects but was not sure if the vaccine was human ready. Seeing no way out, he injected the boy and the boy survived. He was the first person to use a vaccine. l. Ignaz Semmelweis: This was the head doctor on the pregnancy wing of the hospital. What he had noticed was that a lot of the patients were getting childbed fever. What was happening was the interns that were working in the morgue below the hospital would come up whenever a delivery needed to be made. However, they would not wash their hands and thus contaminate the mother. Ignaz said that everyone was to wash their hands before coming to deliver and he noticed a significant decrease in the fever. However, he was ridiculed for his hypothesis and he eventually resigned and checked into a mental asylum. There he was beaten to death by a guard. 10. List Koch’s Postulates and describe how they are used to determine the cause of a disease (including the microbiological techniques employed). a. Robert Koch He linked thee disease anthrax to bacteria and was able to prove it with his own postulates which are still used today. i. Most be present in all cases of the infected and none in the living. ii. You must be able to pure culture grow that bacteria. And create more. iii. Reinfection the healthy animal iv. If the animal becomes sick again then try to pure culture grow the bacteria again. v. If all of the required steps are met, then you have related the bacteria to the disease. vi. KOCH’S CONTRIBUTIONS Limitations Techniques and supplies Can’t grow some cells Agar Derived from seaweed Stays solid at 37C Bacteria cant digest Ethics such s reinfection a PetriDish healthy animal Air can still get there Methods for isolating bacteria vii. 11. Be aware of the major fields in microbiology and various job opportunities in these fields. a. Immunology: How the body responds to the virus i. Edward Jenner Developed a vaccination of smallpox 1. Inoculated a small boy down the street ii. Pastur and Roux attenuation: incubate bacterial cultures for long periods of time to weaken their virulence 1. Cholera b. Industrial Microbiology: This is the use of microbes in big business i. Pasteur Process of pasteurization to cure the wine of its bad taste ii. Alexander Fleeming Discovered Penicillin c. Microbial Ecology i. Sergei Winogradsky and Beijerinck pioneered the enrichment cultures ii. Studied soils and found numerous processes such as nitrogen fixation iii. Beijerinck Father or Virology d. Molecular Micro i. Restriction endonucleases and Sanger sequencing. ii. PCR Chapter 2.1 – 2.4 12. Know the terms associated with microscopy. a. Refractive index measure of how greatly a substance slows the velocity of light i. The direction and magnitude of bending are from the refractive indices of two mediums b. NormalThis is the imaginary line drawn towards the center of the lens or medium. i. Every light is bent towards the normal in a microscope c. Focal Point This is the intersection of the light pathways when shining through a lens d. Focal length this the distance between the normal and the focal point. i. Increase the focal length=Decrease in MAGNIFICATION e. Parafocal This is the ability to change lens where under one lens it is in focus and under another more powerful or less powerful lens it is still in focus f. Paricentric exchange lens object is still in the center 13. Define and understand the concepts of magnification, resolution, and refractive index (including the factors that affect them and how). a. Resolution is the ability to tell where two objects are either one or two b. Refractive index measure of how greatly a substance slows the velocity of light c. MagnificationThis is how greatly an image is increased in size: i. Calculated using : ii. Magnificaiton=Objectivelens xeyepiece d. Resolution EquationCreated by Ernest abbe i. d= 0.5(wavelength) (nsin(theta)) ii. d=minimaldistancewhereyoucansti ll tell two objects iii. (nsin(theta))=numericalaperature 1. n=refractive index 2. sin(theta)=numerical aperture iv. Numerical Aperture is the angle at ½ field of view: 1. 2. Decrease (d)=Increase in resolution=decrease wavelength=increase numerical aperture 3. Theta can only be ½ n… so if you increase n you will increase your theta which will increase your resolution 4. Highest Resolution will be when your theta is the greatest and the wavelength is the smallest 14. Describe the attributes and limitations of the microscopes discussed and how they are used. a. Oil immersion Lens When light passes through air and the working distance, some of the rays are lost due to simple refraction by air. Oil, has a greater n than air and this will allow a greater theta. When you place oil on the slide and between the lenses, all the alight that was being lost is not being focused in the lens thus increase the magnification. This will magnify your image to about 1000X. 15. Compare and contrast light and transmission electron microscopes. Electron Light Electron beam allows the wavelength to be Relatively larger wavelength really small 100000 X max 1000X max TransmissionCross Section ScanningAcross surface a. 16. Explain the preparation and staining of specimens a. Why? i. Increases Visibility ii. Accentuates the creatures outside and insides iii. Preserves the specimen b. FixationProcess by which an organisms physical and structures are fixed in 1 position i. Heat Fixation Routine use with bacteria 1. Preserves overall morphology for a long time however, it may distort the bacteria ii. Chemical Fixationused for more delicate structures 1. Can preserve both morphological and internal structures this cause the cell to completely freeze 17. Compare and contrast the characteristics of basic and acidic dyes. a. Dyes have two things in common i. Chromphore groups this allows it to have color ii. PolarityThis allows it to stick to the structure iii. Acidic dies and basic dies don’t have much difference, the only thing is, and when the specimen is acidic you use an acidic die and visa versa for basic. 18. Distinguish between simple staining, differential staining, and negative staining. a. Simple StainUse of only one b. Differential SatinUse of multiple stains to highlight different structures c. Negative Stain This highlights the background and leaves the bacterium as is. 19. Know the steps of the Gram stain and understand how it differentiates gram positive and gramnegative bacteria. a. The gram stain is very useful because it is a quick and easy way to separate bacteria. b. It separates it based on the absence or presence of peptidoglycan. i. Gram positive Peptidoglycan is present ii. Gram Negative Peptidoglycan is absent (Little present) c. Steps i. Stain mixture with Crystal Violet 1. This cause the peptidoglycan to absorb the CV ii. Stain with an Iodine Solution 1. This acts as a mordant which acts as a solution that can make CV stay bound to the Peptidoglycan. 2. Since there is not much pep in the negative cells, the CV will not stick as well. iii. Wash with Alcohol 1. This will remove the CV from the negative cells because as the pep shrinks and contracts, the CV is expelled and then washed away by the alcohol 2. In the positive cells, the peptidoglycan shrinks but because it has so much more pep, it retains the CV iv. Counterstain with Safin 1. This will turn the negative cells a reddish pink, this is so you can identify them. 2. 20. Describe the acidfast stain, endospore stain, capsule stain, and flagella stain. a. Acid Fast stain Since some bacteria membranes are lipid heavy, such as mycobacterium, the stain will not penetrate the membrane and thus you will not see anything. So when you drive the color into the membrane it is used in acidic conditions. b. Endospore Stain an endospore is a tough little booger that can resist more stains including a lot of environments. This technique uses a double heated staining technique where the endospore is one color and the vegetative cell wall is another c. Capsule Stain Negative stain!!! Colorless capsule against a dark background d. Flagella Stain These are really thin and thus the use of mordant increases the thickness of the flagella making them visible Chapter 7.5 21. Compare and contrast defined and complex media. a. 22. Distinguish between general purpose, enriched, minimal, selective, and differential media. a. General Media Supports the growth of many organisms and contains a lot of nutrients b. Enriched mediaSpecial mediahas some special component i. Example: Blood agar c. Minimal media only the bare essentials inorganic salt, a simple carbon source and H20 d. Selective Mediafavor growth of some and not others has some special nutrient that can allow one organism to grow. 23. Define and describe a “pure culture” of bacteria, and know the techniques used to isolate one. a. Pure Culture This is a population arising from a single cell i. Allows for the study of one microorganism b. Techniques: i. Streak Plate This is the one we did in lab 1. ii. Spread PlateThis is where a diluted volume of culture is transferred to an agar plate and then spread out. iii. Pour Agar Plate This where the diluted volume of specimen is mixed in with the agar and then poured into a petri dish iv. BOTH PROVIDE: 1. Can count the isolated colonies a. Number of colines X (Dilution Exponent)=# of C b. 50 X 10 =50000 bacteria 24. Describe aseptic technique. a. This is technique where inoculating other media does not contaminate the solution when doing so. b. 25. Describe microbial growth on solid surfaces and its significance in identifying bacterial species. a. Species form characteristic colonies b. Differences in growth rate from edges to center is due to i. Oxygennutrients and toxic products 26. Chapter 3.1 – 3.5 27. Recognize and know the cell morphologies (shapes and arrangements) of prokaryotes. a. Shape: i. Cocci and Bacilli 1. CocciSpheres a. Diplococcic two cocci b. StreptococciChain c. Staphylococcigrapelike clusters d. Tetrads4cocci in a square e. Sarcine cubic configuration of bacilli 2. Bacillirods a. Cocobacillivery short rods b. Viorios resemble rods, comma shapes c. Spirillia rigid helices d. Spirochetes flexible helices b. Arrangement determined by the plane of division and degree of separation after division c. Other shapes and arrangements i. Filamentous 1. Myceliumnetwork of long multicellular filaments 2. Pleomorphicvariable in shape which means no cell wall 3. Archeapleomorphic, branched, flat, square, and other unique shapes 28. Know the size ranges for bacteria, viruses, and eukaryotic cells. a. Euk 0.8 microns hundreds of microns i. Largest is ostrich egg ii. Longest is the neuron in the giraffe b. Bacteria/ Archeca i. 0.2750 microns c. Virus i. 0.01microns1micron ii. mega virus 29. Understand the relationship of the size of the cell and its surface area to volume ratio. a. Because cells are so small, this means that they have a greater surface to volume ratio. This means amplified metabolic processes which also means more reproduction. 30. Describe the structure and functions of the plasma membrane of Bacteria and be able to label it. a. Characters: i. Enclose cytoplasm ii. Selectively permeable iii. Interacts w/ external environment 1. Receptors for detection and interaction b. Functions: i. Interact with environment ii. Enclose cytoplasm iii. Act as a gate keeper iv. Transport systems v. Metabolic processes 1. ETC for bacteria on the membrane c. Structure: i. Phospholipid bilayer 1. Hydrophilic head 2. hydrophobic head 3. As the saturation increases so does the temperature of the environment it is in. Hot spring, very saturated to remain together. d. Proteins and other things i. Hapinoids these stabilize the membrane ii. Proteins get to membrane by translocation 1. Must be amphipathic 2. Must remain in a micro domain 3. Peripheral remains on the outside of proteins. a. 2030% 4. Integral Proteins embedded a. 7080% 31. DISEASES* 32. For each of the microbial diseases listed below, be able to briefly describe the following: a. cause (name of bacterium or virus) b. general characteristics of the microbe (bacterium – Since the and shape, virus – type of genome [DNA or RNA] and shape) c. route of transmission d. Characteristic symptoms. Tuberculosis e. Mycobacterium tuberculosis (Mtb) f. general characteristics of the microbe (bacterium – Since this is a Mycobacterium, an acid fast stain will work the best rather than the gram stain. and Rod virus – DNA) g. TB is contracted through the air. Whenever an infected patient coughs, sneezes, or exhales with some force, the bacterium is expelled into the air. Then the bacterium is simply breathed in by the next person. The bacterium must first make it pass all of the defense systems in your throat and mouth to reach the air sacs. This is an aerobic virus which means it needs a lot of oxygen to survive. h. Symptoms: a. Coughing that lasts three or more weeks b. Coughing up blood c. Chest pain, or pain with breathing or coughing d. Unintentional weight loss e. Fatigue f. Fever g. Night sweats h. Chills i. Loss of appetite Bubonic Plague i. Yersinia pestisgeneral j. Gramnegative, rodshaped coccobacillus, a facultative anaerobic bacterium that can infect humans and animals) k. Route of transmission The bacteria starts in rats and rodents and is transferred from rodent to rodent by fleas. Once a flea bites a hume a terrible blacks pot forms on the skin a large swelling lymph node results as well(bubo hence the name) If the bacteria reaches the lungs, the victim can develop pneumonia. From there, you can transmit it as easy as TB. l. People infected with plague usually develop “flulike” symptoms after an incubation period of 37 days. Typical symptoms are the sudden onset of fever, chills, head and bodyaches and weakness, vomiting and nausea. Smallpox a. contagious disease caused by the variola virus, a member of the genus Orthopoxvirus, b. Smallpox is a doublestranded, 135 to 375kilobase (kb) DNA virus that replicates in the cytoplasm of the host cell and forms Btype inclusion bodies c. d. The smallpox virus is transmitted mainly through the airborne route and adheres via droplet spread of viral particles onto the mucosal surfaces of the oropharyngeal and respiratory tract. This transmission occurs through close personal contact (eg, facetoface within 6 ft, household contact) for extended periods. Respiratory spread over long distances (eg, from one hospital floor to another) has been reported. Exposure to clothing or blankets contaminated with infected material can also result in disease.[11, 12] e. Symptoms i. Formation of furuncles and/or abscesses secondary to bacterial infection ii. Sepsis iii. Pockmarks iv. Blepharitis v. Conjunctivitis vi. Corneal ulceration vii. Keratitis viii. Blindness (1% of cases) Rabies a. Rabies virus belongs to the order Mononegavirales, viruses with a nonsegmented, negativestranded RNA genomes. Within this group, viruses with a distinct "bullet" shape are classified in the Rhabdoviridae family, which includes at least three genera of animal viruses, Lyssavirus, Ephemerovirus, and Vesiculovirus. The genus Lyssavirus includes rabies virus, Lagos bat, Mokola virus, Duvenhage virus, European bat virus 1 & 2 and Australian bat virus. b. Bite by an infected animal c. There may be also discomfort or a prickling or itching sensation at the site of bite, progressing within days to symptoms of cerebral dysfunction, anxiety, confusion, agitation. As the disease progresses, the person may experience delirium, abnormal behavior, hallucinations, and insomnia. Pertussis a. Bordetella pertussis b. c. WHOOPING COUGH d. Paroxysms (fits) of many, rapid coughs followed by a highpitched "whoop" e. Vomiting (throwing up) during or after coughing fits f. Exhaustion (very tired) after coughing fits g. Coughing or sneezing or when spending a lot of time near one another where you share breathing space. Many babies who get pertussis are infected by older siblings, parents, or caregivers who might not even know they have the disease. *Even if we do not cover these diseases in class, you are still responsible for the Information. UNIT 1 ANIMATIONS TO WATCH: http://highered.mheducation.com/sites/0073402400/student_view0/index.html : Chapter 3 “Prokaryotic Cell Shapes” NOTE: Unless otherwise stated, you are responsible for all of the unit objectives even if they are not covered in class (see textbook). Also, these objectives only include the lecture topics. Objectives for any supplemental material covered on outofclass assignments will be announced.
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