Unit 1 Study Guide - Summary Prescott\'s Microbiology PDF

Preview

Summary

midterm exam 1 study guide with notes from the book and lecture ...

Description

UNIT 1 STUDY GUIDE (MICRO 305, SPRING 2012) OBJECTIVES: Chapter 1 Define “microorganism” and describe the types studied by microbiologists (cellular and acellular). Microorganisms are organisms and acellular entities too small to be clearly seen by the unaided eye  generally going to need a microscope to see them - Generally less than or equal to 1 mm in diameter - Often unicellular (though there are some multicellular microorganisms as well) Some exceptions include: (1) Amoeba that lives on the ocean floor that is an inch in diameter (2) Bacterium that is the size of a head of a fruit fly The Types of Microorganisms studied by Microbiologists: 1. Cellular a. Fungi  such as yeasts and molds b. Protists  such as algae, protozoa, and slime molds c. Bacteria  such as E. coli d. Archaea  such as methanogens 2. Acellular a. Viruses  composed of protein and nucleic acid b. Viroids  composed of RNA c. Virusoids  composed of RNA d. Prions  composed of protein Distinguish between the basic and applied aspects of the science of microbiology. Basic aspects of the science of microbiology: - Concerned with understanding individual groups of microbes - Microbial physiology, genetics, molecular biology, and taxonomy - Understanding microorganisms has improved the understanding of other organisms Applied aspects of the science of microbiology: - Concerned with practical problems and the use of microbes in advantageous ways - Disease, water, food, and industrial microbiology Understand the importance of microorganisms (scope and relevance). - Most populous group of organisms on Earth  5 x 10^30 bacteria on Earth - Microbes are found everywhere on the planet  bacteria has been found up to 10 kilometers into the surface of the Earth and it is predicted that 92% of all bacteria are under the ground - Lay a major role in the recycling of elements (ex: nitrogen, carbon, and sulfur)  microbes contain 50% of all carbon and 90% of all nitrogen - Source of nutrients  75% of our oxygen comes from bacteria and algae - Some carry out photosynthesis  it is thought that the first organism to perform photosynthesis was cyanobacteria

-

Most beneficial or benign, though some are detrimental Excellent tools for study Influence all other living things

Compare and contrast prokaryotic and eukaryotic microbial cells. (1) Prokaryotic: do not have a true membrane-bound nucleus (2) Eukaryotic: membrane bound nucleus, other membrane-bound organelles, generally larger in size and more complicated morphologically Explain how the Universal Phylogenetic Tree was developed. The 3 domains and the Universal Phylogenetic Tree were developed from comparing the DNA sequencing of a gene encoding for the production of small, ribosomal RNA. Process: (1) Isolated DNA from cells (2) Located the gene encoding for ribosomal RNA on the DNA (3) Conducted a PCR to determine the DNA sequencing (4) Performed a sequence analysis and aligned the rRNA gene sequences (5) Generated a phylogenetic tree  resulted in the 3 domains: Eukarya, Archaea, and Bacteria Distinguish between the three domains of life and understand their relatedness. *All three domains share the same common ancestor known as LUCA (Last Universal Common Ancestor), which serves as the root of the phylogenetic tree A. Domain Bacteria: - Prokaryotes - Unicellular - Cell walls containing peptidoglycan - Some live in extreme environments - Abundant in soil, air, water, and on/in other organisms B. Domain Archaea: - Prokaryotes - Differ from Bacteria in that they have a unique rRNA sequences - Cell walls lack peptidoglycan - Have unique membrane lipids (that are very similar to sterols) - Many live in extreme environments - Some have unusual metabolic processes C. Domain Eukarya: - Eukaryotes Describe the microorganisms of the three domains. *All organisms in the domains Bacteria and Archaea are microorganisms Domain Eukarya: microorganisms from Eukarya are generally larger than those from Bacteria and Archaea A. Fungi - Yeasts - Molds

B. Protists - Protozoa - Algae - Slime molds - Water molds Be familiar with the current theories of microbial evolution and the evidence used to support these theories. 3.8 – 3.5 billion years ago the first cells appeared 3.5 billion years ago  fossils were found of primitive, filamentous microbes 2.5-2.0 billion years ago  the first eukaryotic cells first appear How did Microbes Evolve? Mutation of genetic material  new genotypes  natural selection Bacteria and Archaea are haploid and can increase genetic diversity by horizontal gene transfer within the same generation Evidence: - Swartkoppie and Archaean Apex chert - Microbial fossils have been found that are 3.5 billion years old but the fossil record is sparse - Also through indirect evidence and the scientific method as well as the study of extant organisms Define the prokaryotic “species” and the bacterial strain. Prokaryotic species: a collection of strains that share many stable properties and differ significantly from other groups of strains Microbial strain: a strain consists of the descendants of a single, pure microbial culture *One strain is always designated as the “type strain”:  Usually one of the first ones made  Not always the most representative member of the species  Permanent example  Often are the most fully characterized Explain how microorganisms are named. Microorganisms are named based off of a binomial nomenclature in which the first name is the organism’s genus name and the second is the organism’s species name  They are often very descriptive as well and their Latin and/or Greek translations often tell you about their appearance or what they are used for Know the contributions of the scientists discussed to the science of microbiology. (1) Robert Hooke - In 1665 he was the first to discovery microorganisms when he looked at blue mold growing on a leather shoe underneath a microscope  he drew what he saw = the first accurate drawing of a microorganism - He described the fruiting structures of molds

(2) Antony van Leeuwenhoek - First to discover and accurately describe bacteria (1674-1676) (3) Ferdinand Cohn (1828-1898) - Known as the Father of Bacteriology - Was the first to use the genus name Bacillus - Classified bacteria based on shape - Discovered bacterial endospores (4) Joseph Lister (1827-1912) - Developed a method of surgery to prevent microorganisms from entering wounds and reduced the number of postoperative infections in his patients (5) Ignaz Semmelweis (1847) - Hand-washing to prevent “childbed fever”  made the medical students coming up from working in the morgue to wash their hands before delivering babies in order to help prevent “childbed fever” - It helped but then the students refused to wash their hands Describe the experiments that led to the downfall of the theory of Spontaneous Generation. *Spontaneous generation: the belief that living organisms can development from nonliving or decaying matter (1) Francesco Redi (1668) - Disproved spontaneous generation for large organisms with his decaying meat and fly experiment: flies were not produced by the meat when the jar was covered by a cork or by only gauze (2) John Needham (1748) - His experiment: mutton broth in a flask  boiled it  sealed it - Result: the broth became cloudy from the growth of bacteria (3) Lazzaro Spallanzani (1768) - His experiment: broth in a flask  sealed the flask  then boiled for 45 minutes - Results: no growth of microorganisms (4) Louis Pasteur (1861) - Disproved spontaneous generation!! - His experiment: nutrient solution in a flask with a long, curved neck exposed to the open air still, boiled the flasks and the one with the neck still intact remained sterile – when the neck on the second flask was broken growth occurred (5) John Tyndall (1820-1893) - Showed that dust carries microorganisms  Showed that if dust was absent, nutrient broths remained sterile (even if exposed to air directly) - Also was the first to show evidence of the existence of exceptionally heatresistant forms of bacteria List Koch’s Postulates and understand how they are used to determine the cause of a disease (including the microbiological techniques employed). Established the relationship between Bascillus anthracis and anthrax Used criteria from his teacher Henle  know known as Koch’s postulates and still used today to link pathogens to the diseases they cause Koch’s Postulates:

1. The suspected pathogen should be present in all dead organisms (or in all cases of disease) and absent in all healthy organisms a. Observe blood/tissue under the microscope 2. The suspected pathogen should be grown in a pure culture a. Streak agar plate with sample from either diseased or healthy animal 3. Cells from a pure culture of the suspected pathogen should cause disease in a healthy organism a. Inoculate healthy animal with cells o the suspected pathogen 4. The pathogen should be isolated and compared to the original (shown to be the same as the original) a. Remove blood or tissue sample and observe by microscopy Inventions/Developments from Koch: - Agar  solid medium to grow bacteria on - Petri dish - Nutrient broth and nutrient agar - Methods for isolation microorganisms List and define the major fields of microbiology and be aware of the various job opportunities in these fields. 1. Medical microbiology 2. Industrial microbiology  using microorganisms for fermentations, process of pasteurization, penicillin 3. Agricultural microbiology 4. Education microbiology 5. Immunology  Vaccinations and attenuation of bacteria (pathogens lose their ability to cause disease) 6. Microbial physiology 7. Microbial ecology  nitrogen fixation of microorganisms in soil and chemolithotropy 8. Microbial genetics, bioinformatics, and molecular biology  DNA is genetic material, restriction endonucleases, recombinant molecules, DNA sequencing, PCR

Chapter 2.1 – 2.4 Know the terms associated with microscopy. Define and understand the concepts of magnification, resolution, and refractive index (including the factors that affect them and how). (1) Magnification: the measurement of how much the image can be enlarged - Affected by the focal length: distance between the center of the lens and the focal point at which the light rays are focused by the lens o The shorter the focal length = the greater the magnification - Upper limit of magnification of a light microscope = 1500x (2) Resolution: the ability of a microscope to distinguish between small objects very close together, how clear the image is (clarity)

-

Affected by wavelength: the shorter the wavelength = the greater the resolution Also affected by numerical aperture o Numerical aperture (NA): the measure of light gathering ability o Higher numerical aperture = greater resolution - Upper limit of resolution of a light microscope = 0.2 um (3) Refractive index: a measurement of how much a substance slows down the velocity of light - Factors that affect refractive index are the two medium that form the interface - Direction and magnitude of the bending of light is determined by the refractive indices of the 2 media forming the interface Describe the attributes and limitations of the microscopes discussed and how they are used. Bright-field Microscope: - A dark image against a light/brighter background - Has several objective lenses: parfocal and parcentric Dark-field Microscope: - Image is formed by light reflected or refracted by specimen  produces bright image of the object against a dark background - *Used to observe living, unstained preparations o Used to identify bacteria o Used to observe internal structures in eukaryotic microorganisms - Advantage: don’t have to stain the bacteria to see them = don’t have to kill the bacteria by staining them Compare and contrast light and transmission electron microscopes. A. Light Microscope: light travelling through the air is the radiation source; glass lens - Source of contrast: differential light absorption - Upper limit magnification: 1,000 -1,500 X - Best resolution: 0.2 um B. Transmission Election Microscope: electrons under vacuum replace light as the illuminating beam; electromagnet lens - Electrons scatter when they pass through thin sections of a specimen  denser regions in specimen scatter more electrons and appear darker - The wavelength of an electron beam is shorter than that of light = higher resolution - Magnification: greater than or equal to 100,000 X - Resolution limit: 0.5 nm *Magnification on TEM is better but the resolution of a light microscope at a lower magnification is Note: scanning electron microscope (SEM)  uses electrons reflected rom the surface of a specimen to create a 3-D image of the specimen’s surface features Explain the preparation and staining of specimens. Reasons behind preparation and staining of specimens: - Increases visibility of specimen

- Accentuates specific morphological features - Preserves specimens Fixation: preserves the internal and external structures and fixes them in position on the slide - Heat fixation: routine use with bacteria and archaeons o Preserves overall morphology (shape) but not internal structures o Good because it kills the organism and makes it stick to the slide - Chemical fixation: used with larger, delicate organisms  can preserve internal structures Compare and contrast the characteristics of basic and acidic dyes. *Dyes all have 2 common features: (1) Chromophore groups  chemical groups with conjugated double bods that give dye its color (2) Ability to bind to cells A. Basic Dyes - Dyes with positive charges o Ex: crystal violet, methylene blue, and safranin - Bind to negatively charged structures like proteins and nucleic acids B. Acidic Dyes - Dyes with negative charges o Ex: eosin, rose Bengal, and acid fuchsin - Bind to positively charged structures like lipids NOTE: the surface of most bacteria is negatively charged which is why basic dyes are used more often Distinguish between simple staining, differential staining, and negative staining. A. Simple Staining  only one staining agent is used (Ex: crystal violet stain or methylene blue stain) B. Differential Staining  use more than one dye to preferentially stain features - Used to detect presence or absence of structures - Divides microorganisms into groups based on their staining properties o Ex: gram stain and acid-fast stain C. Negative Staining  typically performed using a black ink fluid such as nigrosin - When viewed under the microscope the bacterial cells and possibly their spores appear light against the dark surrounding background Know the steps of the Gram stain and understand how it differentiates grampositive and gram-negative bacteria. 1. Crystal violet (primary stain) for 1 minute  water rinse a. Cells stained purple 2. Iodine (mordant) for 1 minute  water rinse a. Cells remain purple 3. Alcohol (decolorizer) for 10-30 seconds  water rinse

a. Gram-positive cells remain purple b. Gram-negative cells become colorless 4. Safranin (counterstain) for 30-60 seconds  water rinse a. Gram-positive cells remain purple b. Gram-negative cells appear red/pink 5. Blot dry Describe the acid-fast stain, endospore stain, capsule stain, and flagella stain. (1) Acid-fast stain: particularly useful for staining members of the genus Mycobacterium  high lipid content in cell walls (mycolic acid) is responsible for their staining characteristics (2) Endospore stain: heated, double-staining technique  bacterial endospore is one color (blue in lab) and vegetative cell is a different color (pink/reddish in lab) (3) Capsule stain: capsules colorless against a stained background (4) Flagella stain: Mnenta stain applied to increase thickness of flagella

Chapter 6.7 – 6.8 Compare and contrast defined and complex media. A. Defined or synthetic media: media in which all of the component ingredients and their concentrations are known - Ex: medium for E. coli and medium for cyanobacteria B. Complex media: media that contains some ingredients or unknown composition and/or concentration - Ex: Nutrient broth (beef extract and peptone) & Tryptic Soy Broth (tryptone, peptone, glucose, sodium chloride, and dipotassium phosphate) Distinguish between general purpose, enriched, minimal, selective, and differential media. (1) General purpose media: also known as “supportive media” to support the growth (reproduction) of microorganisms - Ex: TSA (tryptic soy agar) (2) Enriched media: a general purpose media supplemented by special blood nutrients - Ex: chocolate agar (3) Minimal media: contains just the minimal necessities for growth of the wild-type - Made up of only inorganic salts, water, and a simple carbon source (4) Selective media: favors the growth of some microorganism and inhibit the growth of others - Ex: MacConkey agar  favors gram-negative bacteria (5) Differential media: distinguishes between different groups of microorganisms based on their biological characteristics - Examples: o Blood agar  hemolytic vs. non-hemolytic bacteria o MacConkey agar  lactose fermenters vs. non-fermenters

Define and describe a “pure culture” of bacteria, and know the techniques used to isolate one. Pure culture: population of cells arising from a single cell – allows for the study of a single type of microorganism - General technique for isolating: a mixture of cells is applied to an agar surface so that individual cells are well separated from each other - 3 Techniques Used: 1. Streak plate  using an inoculating loop to spread a sample of cells on an agar surface; each cell can reproduce to form a separate colony = visible growth or cluster of microorganisms 2. Spread plate  a small amount of the diluted sample is placed in the middle of the agar plate and spread around evenly using a sterile bent rod (or hockey stick) 3. Pour plate  dilutions of the sample are mixed with liquid agar and poured into sterile culture dishes *Note: a countable plate is 30-300 Describe aseptic technique. (1) Flame the inoculating loop in a Bunsen burner (2) Take the top off of the tube containing the bacteria sample and flame the mouth of the tube (pass it quickly through the flame) (3) Dip the inoculating loop into the sample and quickly draw it out (4) Re-flame the mouth/opening of the tube (5) Put the top back on the tube (6) After streaking the plate with the inoculating loop flame it once again **Be able to set up a dilution and calculate cell concentration from a plate count** Describe microbial growth on solid surfaces and its significance in identifying bacterial species. Species of microbes form unique or characteristic colonies on solid surfaces There is a difference in the growth rate from the edges to the center due to: oxygen, nutrients, and toxic products as well as any dead cells that may be present in some areas Descriptions of colonies to do on form, elevation, and margin: - Form  punctiform, circular, filamentous, irregular, rhizoid, and spindle - Elevation  flat, raised, convex, pulvinate, umbonate - Margin  entire, undulate, lobate, erose, filamentous, and curled

Chapter 3.1 – 3.3, 6.6 Recognize and know the cell morphologies (shapes and arrangements) of prokaryotes. (1) Cocci (coccus)  spherical a. Diplococci: pairs b. Streptococci: chains of cocci

(2)

(3) (4) (5)

c. Staphylococci: cubic configuration of 8 cocci d. Tetrads: 4 cocci in a square e. Sarcinae: cube configuration of 8 cocci Bacillus (bacilli)  rod-shaped a. Coccobacilli: very short rods b. Vibrios: rod-like, shaped like a comma c. Spirilla (Spirillum): rigid helices d. Spirochetes: flexible helices Filamentous a. Mycelium: network of long, multinucleate filaments Pleomorphic  variable in shape Archaea shape: a. Pleomorphic, branched, flat, square, or other unique shapes

Know the size ranges for bacteria, viruses, and eukaryotic cells. Eukaryotic cells: 0.8 um – hundreds of um Bacteria/Archaea: 0.2 um – 750 um Viruses: 0.01 um – 1um Understand the relationship of the size of the cell and its surface area to volume ratio. The smaller the cell, the LARGER the surface area to volume ratio Example Relationship: A cell with a radius of 1 um SA (4πr2) = 12.6 um2 V (4/3 πr3) = 4.2 um3  Therefore, SA ...