Prescott Microbiology 11th Edition Textbook Summaries (PDF)

lOMoARcPSD|38091128 Chapter 1-3 - Summaries from Prescott Microbiology 11th edition textbook Microbiology (Universiteit Stellenbosch) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or univ...

lOMoARcPSD|38091128 Chapter 1-3 - Summaries from Prescott Microbiology 11th edition textbook Microbiology (Universiteit Stellenbosch) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 CHAPTER 1: INTRODUCTION [20 MARKS] 1. What are the similarities between archaea and eukaryotes?  Both have intron in their genes  Both lacks peptidoglycan in their cell walls  The gene translation mechanism for both starts with methionine 2. What are characteristics of archaea that makes it unique?  Can tolerate extreme environments of up to 120 degrees Celsius  Some undergo methanogenesis: the formation of methane  In the lipid composition of the membrane, the C-atom on the glycerol is linked to an alkyl chain via an ether linkage 3. What are the similarities between bacteria, archaea, and eukaryotes?  Has DNA as the genetic bacteria  Has a membrane-bound cytoplasm  Ribosomes are present  Shares similar basic metabolism 4. What are the differences between prokaryotes and eukaryotes? Prokaryotes Eukaryotes  No membrane-bound nucleus – its  Double membrane-bound nucleus and “nucleus” = nucleoid membrane-bound organelles  Small compared to eukaryotes  10x larger than prokaryotes  Simple DNA structure –  DNA is more complex and are circular/plasmids compacted into histones  Peptidoglycan present in cell wall  No peptidoglycan in cell wall 5. Define/describe what histones are. Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order DNA into structural units called nucleosomes. 6. What is spontaneous generation? It is the early theory of how life forms came about, and it was believed that living organisms developed from non-living matter. 7. Discuss how scientists, through their experiments, disproved spontaneous generation. Downloaded by Florence ([email protected])  lOMoARcPSD|38091128  Francesco Redi  Disproved SG for large animals  Showed that maggots on decaying meat came from fly eggs  Lazzaro Spallanzani  He transferred water and seed broth in a flask, sealed it and the boiled it  There was no growth of microbes if flask remain sealed  Concluded that air carried germs to the medium and air may be required for germs to grow  Theodore Schwann  He allowed air to enter the flask containing a sterile nutrient solution  Flask was passed through a red-hot tube  The flask remained sterile  Schroeder and von Dusch  Allowed air to pass through sterile cotton wool to enter the flask  Flask remained sterile  Louis Pasteur  He transferred broth into two flasks, boiled it and melted a portion of the flask to create a curve-neck flask  First flask remained intact. Second flask’s neck breaks  Broth remained sterile in first flask. Microbes are trapped in curved part of the flask  Growth occurred on the second flask  John Tyndall  Showed that if dust is absent, nutrient broths remained sterile, even if exposed to direct air  This is evidence for the existence of heat-resistant forms of bacteria 8. Distinguish between pasteurization and tyndallisation. Pasteurization is the process of slowing down the growth of microorganisms and reducing their number. Tyndallisation is the sterilization method aimed at killing bacterial cells through repeated heating. 9. What are the contributions made by the following people to the field of Microbiology?  Louis Pasteur – disproved spontaneous generation completely + developed vaccine for chicken cholera, anthrax, and rabies  Joseph Lister – developed a system for antiseptic surgery to prevent wound/surgical site infections  Robert Koch – introduced postulates to identify the causative agents of diseases + developed microbe isolation techniques + introduced the use of nutrient broth for growing cultures  Richard Petri – introduced the use of Petri dishes on which to grow microbial cultures  Edward Jenner – introduced a vaccine for smallpox (quite unethically) 10. Was Koch’s general postulates used to prove the association between SARS-CoV-2 and COVID- 19? Motivate your answer by briefly discussing Koch’s general postulates and propose how scientists could have made the association. Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 No! This virus is extremely transmissible and deadly. To prove Koch’s postulates, the microbe must be isolated and grown in a culture. Growing such deadly viruses are deemed unethical. Therefore, Koch’s general postulates could not have been used to make the association. Koch’s general postulates:  The microbe must be present in every case of the disease and absent in healthy organisms  The suspected microbe must be isolated and grown in a pure culture  The same disease must result when the isolated microbe is inoculated into a healthy host  The same microbe must be isolated again in the diseased host Hence, why doing this shit is wayyyy too unethical. Imagine inoculating a human with covid. Imagine!! However, Koch’s molecular postulates could’ve been used to prove the association:  The phenotype under investigation should be associated with pathogenic members of a genus or pathogenic strains of a species  The specific inactivation of the gene(s) associated with the suspected virulence trait should lead to a significant loss in virulence  The reversion or allelic replacement of the mutated gene should lead to the restoration of pathogenicity  The gene, which causes virulence, must be expressed during infection ------------------------------------------------------------------------------------------------- CHAPTER 2: MICROSCOPY [15 MARKS] 1. Distinguish between refraction and a refractive index. Refraction is the bending of a wave through a given medium where its speed is different. Refractive index is the measure of how greatly a substance slows the velocity of light. 2. Distinguish between focal point and focal length. The focal point (F) is the position at which all light rays from a distant light source are focused. The focal length (f) is the distance between the centre of the lens and the focal point. 3. Define/describe the following terms:  Parfocal – the image must stay in focus as the objective lenses are changed  Resolution – the ability of a lens to distinguish between two subjects that are close together  Working distance – the distance between the objective lens and the slide 4. Differentiate between bright field microscopes and dark field microscopes. Bright field microscope Dark field microscope Downloaded by Florence ([email protected])  lOMoARcPSD|38091128  Views fixed, stained/unstained  views living, unstained cells specimens  internal structures of larger cells can  Not able to view detailed internal be viewed structures and cell shapes  cell shape can be distinguished  forms dark image against light  image s formed by light that’s background reflected/refracted by the specimen  has several objective lenses  forms a light image against a dark background 5. Differentiate between phase contrast microscopes and differential interference contrast. Phase contrast microscope Differential interference contrast  Views stained cells  Live, unstained specimen are  Allows smalls differences in the brightly coloured and 3D refractive index of cells to make it  2 beams of light at 90˚ combine to visible form image after passing through  Two types of lights are combined to specimen form image:  Detects differences in refractive 1. Deviated light waves: light from index + thickness of different parts specimen of specimen 2. Undeviated light: light from surrounding environment  Uses condenser annulus and phase plate 6. Differentiate between fluorescence microscopes and confocal microscopes. Fluorescence microscope Confocal microscope  Specimen is stained with  Uses laser beams to illuminate fluorochromes specimen  Specimen is illuminated from the top  Laser beam illuminates a single point  Mercury vapour arc lamp produces to produce sharp 3D image as intense beam of light  Specimen are stained with  Objective lens acts as a condenser fluorochromes  Red cells = dead  Ideal for studying biofilms (cells that  Green cells = alive attach to surfaces)  Fluorescent light emitted by specimen makes image visible 7. Differentiate between transmission electron microscopes and scanning electron microscopes. Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 Transmission electron microscope Scanning electron microscope  Electrons pass through specimen  Electrons are emitted by object’s  Used to study detailed 3D internal surface structures of a cell/virus  Used for surface structure analysis  High vacuum is used to obtain a  Air-dried material can be examined clear image directly  Specimens must be very thin (20-  Specimen are fixed, dehydrated, and 100nm) dried to preserve surface structure +  Specimens are chemically fixed prevent collapse of cells  Specimens are stained with  Specimen are exposed to high electron-dense materials (Pb and U) vacuums  Scans narrow, tapered electron beams over specimen to create 3D image 8. Define/describe what fluorochromes are. Fluorochromes are photoreactive chemicals/compounds that absorb light energy of a specific wavelength and re-emits it at a longer wavelength. 9. Distinguish the difference between shadowing and freeze etching techniques. Shadowing is the application of a thin layer of heavy metal on only one side of the specimen by evaporation at ~45˚. The coated area is dark and is useful to study viruses, flagella, and DNA. Freeze etching technique is the procedure of rapidly freezing cells in liquid nitrogen. The cells become brittle and breaks. The exposed surfaces are shadowed and coated with layers of platinum and carbon to form replicas of the surface. *Both techniques are applicable to TEM 10. Tabulate and compare the light and transmission electron microscopes (0nly 3) Feature Light microscope Transmission electron microscope Highest practical ~1 000 – 1 500 Over 10 000 magnification Best resolution 0.2μm 0.2 nm Radiation source Visible light Electron beam Medium of travel Air High vacuum Type of lens Glass Electromagnet Source of contrast Differential light Scattering of electrons absorption Focusing mechanism Adjust lens Adjust current to the position magnetic lens mechanically Method of changing Switch the Adjust current to the magnification objective lens or magnetic lens eyepiece Specimen mount Glass slide Metal grid (usually copper) CHAPTER 3: BACTERIA [25 MARKS] Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 1. Briefly discuss the significance/functions of the following structures in bacterial cells:  plasma membrane  surrounds the cytoplasm  controls the flow of nutrients into the cell  involved in the transport of molecule  cell wall  protects against toxic substances  is the site of action of several antibiotics  contains electron transport proteins  capsule  helps pathogens withstand phagocytosis  protects against desiccation and toxic substances  glycocalyx  helps with attachment  collective term for capsule and slime layer  slime layer  helps with the gliding function in some bacteria  S-layer  Protects against ion and pH fluctuations, osmotic stress, and predacious bacteria  Helps maintain shape and rigidity of the cell  Cytoplasm  The material that lies between the plasma membrane and nucleoid  Consists largely of water  Cytoskeleton  Determines cell shape  Participates in cell division  Localizes proteins in certain areas  Inclusion bodies  Storage of carbon, energy, and inorganic compounds  Maintains osmotic pressure  Allows for buoyancy of cells in water  Gas vacuole  Helps bacteria to float  Ribosomes  Site of protein synthesis  Cytoplasmic ribosomes make proteins that are destined to stay in the cell  Plasma membrane associated ribosomes make proteins that reside in cell envelope, or which are transported out of the cell  Nucleoid  Stores genetic information of cell  Consists of DNA, RNA, and proteins 2. Discuss the Fluid Mosaic Model and list its associated proteins Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 The FMM describes membrane structures. The plasma membrane is composed of a phospholipid bilayer within which proteins float. Peripheral proteins make up about 20-30% of the total protein composition of the bilayer. It is loosely connected to the membrane and can easily be removed Integral proteins make up about 70-80% of the total protein composition of the bilayer. It is embedded in the membrane and consist of hydrophobic and hydrophilic parts. Transport proteins are used to move materials into/out of the cell. 3. Differentiate between hopanoids and mesosomes. Hopanoids are sterol-like molecules which are made from the same precursor as steroids, and it stabilizes the membrane. Mesosomes are folded invaginations of the plasma membrane. It is involved in cell division and chromosome replication. 4. Peptidoglycan is composed of many identical subunits. List the compounds that comprise these subunits and explain how these units are linked to form an enormous, mesh-like polymer. Note: peptidoglycan gives shape to the cell The subunits of peptidoglycan:  N-acetylmuramic acid (NAM)  N-acetylglucosamine (NAG)  D-glutamic acid  D-alanine  Meso-diaminopimelic acid How these units are linked: A peptidoglycan polymer is formed by linking peptidoglycan subunits to form a peptidoglycan strand. The backbone of peptidoglycan is composed of alternating NAM and NAG residues Direct cross-link: connects a carboxyl group on an amino acid on one subunit to an amino group of another subunit Indirect cross-link: involves a peptide interbridge which is essentially a short chain of amino acids (eg. Glycine) that bonds between the two chains. 5. Differentiate between Gram-positive and Gram-negative bacteria. Gram positive Gram negative  Thick peptidoglycan layer  Thin peptidoglycan layer  Contains teichoic acid  Contains lipopolysaccharides (LPS)  Small periplasmic space  Larger periplasmic space  Contains exoenzymes in periplasmic  Houses various enzymes in space that degrade polymeric periplasmic space nutrients  Proteins on the surface are involved in virulence and attachment Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 6. Distinguish between teichoic acid and lipopolysaccharide. Refer to the composition and function of each component. Teichoic acid is a polymer of glycerol and ribitol joined by phosphate groups. It is linked to peptidoglycan or to membrane lipids and it contributes to the negative charge of the cell. Teichoic acid function:  Helps create and maintain the structure of the cell envelope  It is important during cell division  Protects the cell from harmful substances in the environment  It functions in ion uptake  Binds pathogenic bacteria to host tissue Lipopolysaccharides (LPSs) are complex molecules that contain lipids and proteins. It consists in three parts: 1. Lipid 2. Core polysaccharide 3. O side chain LPS function:  Responsible for negative charge of membrane  Stabilizes the membrane  Acts as a toxin (endotoxin)  Causes an immune reaction in the host  Plays a role in attachment 7. Define/describe the following terms:  Protoplast – bacterial cell whose cell wall has been removed  Spheroplast – bacterial cell that has a partial loss of its cell wall  Magnetosomes – iron-rich magnetic particles that are used to direct sediments  Episomes – plasmids that are integrated into the chromosome and replicates with the chromosome 8. Distinguish between pili and fimbriae. Fimbriae Pili  Short, thin hair-like appendages  Longer, thicker hair-like appendages  3-10nm in diameter  9-10 nm in diameter  Visible with electron microscope  Responsible for the transfer of  Responsible for attachment to genetic material surfaces, gliding motility and twitching motility 9. Distinguish between plasmid and chromosome. Plasmids are shorter extrachromosomal double-stranded DNA molecules that can exist independently of the chromosome. Chromosomes are thread-like structures in which DNA is tightly packaged within the nucleus. DNA is coiled around proteins called histones, which provide the structural support. Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 10. Discuss the different types of plasmids.  Conjugative plasmid: responsible for genes of pili and transfers copies of DNA  R-plasmid: responsible for the genes for antibiotic resistance and is not integrated on host chromosome  Col-plasmid: can destroy other bacteria and are effective against E.coli  Virulence plasmid: carries virulence genes, thus making host cell more pathogenic  Metabolic plasmid: carries enzymes that degrade substrates 11. Tabulate and compare bacterial flagella and archaeal flagella Bacterial flagella Archaeal flagella  Long, thin filament  Thinner than bacterial flagella  Filament is a hollow, rigid cylinder  Not hollow containing flagellin protein  Composed of more than one type of  Responsible for movement, flagellin subunit swarming, attachment and plays a  Hooks are longer than bacterial role in virulence factors hooks. Difficult to distinguish from  Some have protein sheath around filament flagella  No basal body identified 12. Briefly discuss the synthesis of the filament of flagella  Various genes are involved  Flagellin are transported through the core of the basal body  Flagellin aggregates at the end. Leads to growth at the tip  An example of self-assembly 13. Distinguish between positive and negative chemotaxis. Positive chemotaxis occurs when the bacterium exhausts the local supply of nutrients and swims outward, following the attractant gradient that they’ve created. Negative chemotaxis occurs when bacteria move away from the repellent. An example hereof is when E.coli swims away from acetic acid. The concentrations increase clockwise from 0M to 3M acetate. 14. (Illustrate and) describe the components of the bacterial endospore structure. Gram-positive bacteria forms endospores as a survival mechanism that allows the bacterium to produce a dormant cell that will survive until conditions become favourable and vegetative growth resumes. Endospores show incredible resistance to environmental factors like UV light, drying, chemicals and irradiation. Structure:  Nucleoid is saturated with acid-soluble DNA binging proteins  Core contains normal cell structures and are metabolically inactive  Inner membrane surrounds the core  Cell wall  Cortex is composed of peptidoglycan  Outer membrane is composed of a phospholipid bilayer  Coat contains several protein layers, making is impermeable  Exosporium has a thin covering of glycoproteins Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 15. (Illustrate and) discuss the sporulation process. Step 1: axial filament formation  DNA replication occurs  Spore septum begins to isolate the newly replicated DNA and a small portion of the cytoplasm Step 2: septum formation and forespore development  Plasma membrane starts to surround the replicated DNA and cytoplasm  Septum forms. Visible by the infoldings of the plasma membrane into the cell lumen  Spore septum surrounds the isolate portions to form forespore Step 3: engulfment of forespore  Forespore is entirely engulfed by the membrane of the mother cell as it proceeds to grow Step 4: cortex formation  Peptidoglycan layer forms between the two membranes  Dipicolinic acid and calcium accumulates in large quantities Step 5: coat synthesis  A thick spore coat forms around the outer membrane, making the endospore resistant to many harsh chemicals Step 6: spore maturation  New spore loses its water and becomes highly dehydrated  All that remains in the spore is DNA, few RNA, ribosomes, and enzymes Step 7: lysis of sporangium  Endospore is released from the cell  Can remain dormant for 1 000 years *remember diagram 16. Explain the shift from an endospore to a vegetative cell.  Activation  Prepares endospore for germination  Results from treatments like heating  Germination  Environmental nutrients are detected  Spore swells, leading to the rupture/absorption of the spore coat  Increased metabolic activity  Outgrowth  Emergence of vegetative cell Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 17. Various materials make up different types of archaea cell walls. Illustrate the different types of archaeal cell walls that differ with regards to their material composition. *Drawings!! 18. Discuss the difference between archaeal cell wall and bacterial cell wall. Archaeal cell wall Bacterial cell wall  Has N-acetylglucosamine  Has N-acetylglucosamine  Has beta (1-3) glycosidic  Has beta (1-4) glycosidic bonds bonds  Only has L-amino acids  Have L- and D-amino acids  Has N-acetylalosaminuronic  Has N-acetylmuramic acid acid  Phospholipids have ester  Phospholipids have ether linkages linkages  All has a peptidoglycan layer  Some has a layer of pseudomurein ---------------------------------------------------------------------------------------------------------- CHAPTER 3.3 AND 11.1: NUTRITION AND TRANSPORT [10 MARKS] 1. Distinguish between group translocation and active transport Active transport Group translocation  The uptake of molecules against a  transport of a substance across a concentration gradient membrane that occurs together with  Requires metabolic energy chemical modification of the  Bacteria uses a proton gradient to substance drive the transport of molecules  requires metabolic energy  pumps nutrients into the cell and  common sugar transport for solutes out of the cell anaerobes and facultative anaerobes  transports a variety of sugars while phosphorylating them  Enzyme I and heat stable proteins (HPr) are non-specific components  Enzyme II has 3 subunits (IIa, IIb, IIc) which are specific for sugar transfer  P-group is transferred to enzyme II with the aid of enzyme I and HPr  The sugar is transported across the membrane  PEP is the energy source *Know the diagram for group translocation as well Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 2. Distinguish between passive diffusion and facilitated diffusion Passive diffusion Facilitated diffusion  the movement of small  Diffusion of small molecules molecules from a region of using carrier proteins high concentration to a  Rate of diffusion is increased region of low concentration by using carrier proteins  No metabolic energy  No metabolic energy required required  The rate of passive diffusion  Concentration gradient is dependent on the size of drives the movement of the concentration gradient molecules 3. Distinguish between macro and micro molecules Macromolecules are large molecules which often require some form of protein to facilitate its transport into cells. Micro-molecules are small molecules which often diffuse through membranes and into cells without requiring metabolic energy. 4. Distinguish between the different nutritional types of microorganisms. Nutritional type Carbon source Energy source Electron source Photolithoautotroph CO2 Light Inorganic e- donor Photo- Organic carbon Light Organic e- donor organoheterotroph Chemolithoautotroph CO2 Inorganic chemicals Inorganic e- donor Chemolithoheterotroph Organic carbon Inorganic chemical Inorganic e- donor Chemo- Organic carbon Organic chemicals Organic e- donor organoheterotroph 5. Distinguish between primary active transporters and secondary active transporters Primary active transporters use the energy provided by ATP hydrolysis to move substances against the concentration gradient. Secondary active transporters couple the potential energy of ion gradients to transport substances 6. Distinguish between symport, antiport and uniport. Symport is when the substrate and protons move in the same direction Antiport is when protons and sodium move in opposite directions Uniport is when single sugars and amino acids are taken up into the cell Downloaded by Florence ([email protected])  lOMoARcPSD|38091128 7. Describe the process of iron uptake in E.coli and refer to the role of ABC transporters in the process. Iron acquisition  Organisms require iron as it is used in cytochromes and enzymes  Bacteria, such as E.coli secretes siderophores which are known as enterobactin in bacteria (ferrichrome in fungi and aerobactin in plasmids)  Siderophores are produced when iron is limiting in cells  When the iron-siderophore complex binds to the cell, the iron may be released directly or taken up by ABC transporters  Ferric iron is reduced when it’s inside the cell  Iron is unavailable in aerobic environments and is often rate-limiting for cell growth Bacteria secrete siderophores, which can complex with ferric (insoluble) iron and transport it to the cell. They bind to ABC transporters that are embedded in the plasma membrane. After they bind, ATP is consumed and used as an energy source for the uptake of iron through the transporter. The siderophore then leaves the iron, which is reduced to soluble ferrous iron in the cytoplasm ATP-binding cassette (ABC) transporters  Important for active transport  Found in bacteria, archaea, and eukaryotes  Imports and exports substances into/out of the cell  It binds and hydrolyses ATP to drive the uptake of molecules  Uses substrate binding proteins which are located in the periplasmic space of Gram- negative bacteria and in the plasma membrane of Gram-positive bacteria.  Takes up single sugars and amino acids via uniport Downloaded by Florence ([email protected])