BIOL333 Microbiology Past Paper PDF

Topics to cover in the assignment BIOL333 Microbiology 1- An application on bacterial interactions in the environment; Quorum sensing...

Topics to cover in the assignment BIOL333 Microbiology 1- An application on bacterial interactions in the environment; Quorum sensing 2- An application on a pathogenic bacterium in the human body; Dr. Rana El Hajj and its virulence factors Assistant Professor of Molecular Microbiology 3- Hand sanitizers; How do they kill microbes? Are they totally [email protected] safe? 4- Pasteurization of milk, types of bacteria that are killed? Types of bacteria that are still there? 5- Biofilms in Hospitals, examples and effects on health 6- Cholera updates 7- Bioremediation: principle and an application about it Introduction to the microbial world Organisms were classified into either the animal kingdom or the plant kingdom before the scientific community discovered microorganisms in the seventeenth century. Carl Woese developed a new classification system that arranged Attendance is mandatory!!! organisms according to their molecular characteristics and their cellular characteristics. Woese divided three classification groups called domains. A domain is larger than a kingdom. These are the 3 domains: Assessment 1 (7th Week): Midterm Exam 30% of the final grade Eubacteria: Bacteria that have peptidoglycan cell walls. Archaea: Prokaryotes that do not have peptidoglycan cell walls. Eucarya: Organisms from the following kingdoms: Protista: algae and protozoa. Assessment 2 (12th week): Students Presentations (teamwork- 10 Fungi: yeasts and multicellular molds. min per group) 20% of the final grade Plantae: Bryophyta, Pteridophyta and Angiosperms. Animalia: invertebrates and vertebrates.  WHAT IS MICROBIOLOGY? Microbiology is the study of microorganisms (usually less than 1mm in diameter which requires some form of magnification to be seen clearly) and their activities. Viruses, Viroids and Prions are not “organisms” Prokaryotes: Bacteria and Archaea Eukaryotic Microbes: Algae, Fungi and Protozoa Themes in Microbiology and its field Microbiology Basic Applied By Disease Disease Environmentally By organism related Industrial process related related Bacteriology Microbial Immunology Infection Environmental Food & Phycology metabolism Epidemiology control microbiology beverage tech Mycology Microbial genetics Etiology Pharmaceutical Virology microbiology Parasitology Genetic Protozoalogy Engineering  History of Microbiology Although microbes were probably the first living organisms on earth, it was not discovered until the mid. 17th century when the English experimental philosopher, Robert Hooke (1665) described his microscopic observation of fungi and protozoa. In 1680, a Dutch student of natural history named Antony Van Leeuwenhoek was the first to see and describe yeasts and some bacteria. During his lifetime he made more than 250 microscopes, the most powerful of which could magnify only 200-300 times. He sketched bacterial cells as being spherical, rod-shaped or spiral. After Leeuwenhoek, little additional progress in the development of the science of microbiology took place until the the eighteenth century, when the Italian naturalist Spallanzani produced experimental evidence showing that putrefaction of organic substrates is caused by minute organisms that do not arise spontaneously but occured as a result of the multiplication of cells. Spallanzani shows that heating destroys these organisms and that sealing the containers after heating prevents spoilage. The theory of spontaneous generation or abiogenesis (abio= non living, genesis= origin) was proved to be false. The germ theory of disease The strong arguments of the germ theory of disease were expressed by many scientists and the concept of parasitism. Pasteur succeeded in isolating the protozoan causing the (1843-1910) silkworm disease. Later, he isolated the anthrax-causing microbes from the blood of animals that had died of the disease, he grew them in laboratory. At the same time in 1870, the German physician Robert Koch was also interested with the anthrax problem in Germany. He isolated the typical rod-shaped bacteria (Bacilli) from the blood of sheep that died of anthrax. This was the first time a bacterium had been proven to cause an animal disease. A German physicist in Later, Koch discovered the bacteria that caused tuberculosis and cholera. These steps known as Koch's postulates (1890) are: 1. The organism should be present in all animals suffering from the disease and absent from The development of microbiological laboratory techniques all healthy animals. and procedures 2.The organism must be grown in pure culture outside the animal host. 3. When this organism is inoculated into a healthy susceptible host, the animal must Koch and his colleagues developed several laboratory procedures which had develop the symptoms of the disease. tremendous impact on the development of microbiology: 4.The organism must be re-isolated from the experimentally infected animal and proved to Procedures for staining bacteria to make them more easily visible. be identical to the original isolate. Techniques for growing microbes in the laboratory using a culture medium (plural= The steps necessary for identifying the etiological agent of a disease: media). Technique used for growing microorganisms on agar media which permits them to grow separately and permits each cell to divide in order to accumulate in agar surface in the form of a colony. All the cells in the colony are the same; it's assumed that they are the progeny of a single microorganism and hence a subculture derived from single colony represents what the microbiologist calls a pure culture. Working with a pure culture requires an aseptic technique which is also used in surgery to exclude microbes from wounds. The entry of undesirable organisms (contamination) is avoided by applying the aseptic technique (precautionary measures taken to prevent contamination). Microorganism & Microbiology Microorganism Microbiology Living things which individually Study of microorganisms are too small to be seen with the Foundation of modern biotechnology naked eye. Among the many specialized fields of microbiology All of the following may -Virology, Mycology, Bacteriology, be considered Immunology, Microbial Ecology, microorganisms: Biotechnological Microbiology, – bacteria Environmental Microbiology, Food (eubacteria, archaebacteria) Microbiology, Forensic Microbiology, – fungi (yeasts, molds) Molecular Biology – protozoa – microscopic algae – viruses – various parasites  Microorganism Microbes in our lives Food Lactococci Ferment milk Too small Water treatment Germ-rapidly growing cell Such as certain bacteria belonging to the Bacillus species 1. Digest a wide variety of organic material that are present in wastes. 2. Digest waste quickly and completely, without producing significant odors of noxious gas. Has habitat 3. Non-pathogenic. 4. Grow and reproduce quickly and readily in the environmental conditions found in waste disposal systems. Live in population (not alone) Energy Communities are either swimming freely or attached to a Produce methane surface (biofilm) Interact between communities; may either be: Science- laboratories - harmful (can be due to waste product) - beneficial (cooperative feeding efforts-waste→nutrient) Warfare -anthrax Microbes in our lives Microorganism and Food Microorganism and food Some are pathogenic (disease-causing) 1) Prevent spoilage (tempeh, salted fish) Some decompose organic waste 2) Assist in manufacturing of food Some can perform photosynthesis (e.g.Purple sulphur bacteria must fix CO2 to live) Microorganisms and energy Some play a role in the industry (e.g. fermentation to produce 1) Natural gas (methane) ethanol and acetone) 2) Ethanol (biofuel) Some produce fermented food (vinegar, cheese & bread) 3) Bioremediation Some produce products used in manufacturing (cellulase) and treatment (insulin) Microbes and the future 1)Genetic engineering  Microbes and diseases Scientific Names Italicized or underlined. The genus is capitalized, and the specific epithet is with lowercase Could be as an honor for the scientist A Latin origin e.g. Escherichia coli (E. coli) In intestine - discoverer: Theodor Escherich - describes the habitat (colon/intestine) e.g. Staphylococcus aureus (S. aureus) - Clustered (staphylo), spherical (cocci) On skin - Gold colored colonies (aureus) Naming and Classifying Bacteria (P)/ Bacterium (S) Archaea microorganisms Prokaryotes Prokaryotes Has peptidoglycan cell walls Lack peptidoglycan Linnaeus system for scientific Binary fission Live in extreme nomenclature Utilize organic/inorganic environments chemicals, or photosynthesis Include to obtain energy - Methanogens Each organism has two names: - Extreme halophiles 1)Genus - Extreme thermophiles 2)Specific epithet  Viruses Types of Eukaryotes Too small to be observed with light microscope Multicellular animal parasites Consists of DNA/RNA core Algae Core is surrounded by protein coat Helminths: flatworms and Protozoa Coat may be enclosed in a lipid roundworms Unicellular eukaryote Unicellular/multicellular envelope Viruses are replicated only when Multicellular Absorb or ingest organic eukaryotes they are in living host cell chemicals Has cellulose cell walls Bacteriophage-viruses that infect bacteria May move using Gain energy through Viroids-nucleic acid without protein pseudopods, cilia or flagella photosynthesis coating Prions- Infectious protenacious e.g. Amoeba Produce molecular and particles organic compounds Fungi (singular: Fungus) Microscope Eukaryotes Light microscope Uses light Few types Chitin cell walls Compound light microscopy Use organic chemicals for Darkfield microscopy Phase-contrast microscopy Differential interference contrast microscopy energy Fluorescence microscopy Molds and mushrooms are Confocal microscopy multicellular, consists of mycelia (composed of filaments called hyphae) Yeasts are unicellular  Compound light microscope The image is magnified again by ocular lens Total magnification= objective lens x ocular lens Resolution- ability of lenses to distinguish two points e.g. RP of 0.4 nm can distinguish between 2 points ≥ 0.4 nm Refractive index- Light bending ability of a medium Light may bend in air that it misses the small high-magnification lens Immersion oil is used to keep the air from bending. The microscope immersion oil decreases the light Types of Microscopes refraction, allowing more light to pass through your specimen to the objectives lens. Light Microscope - found in most schools, use compound lenses and light to magnify objects. The lenses bend or refract the light, which makes the object beneath them appear closer. Stereoscope - this microscope allows for binocular (two eyes) viewing of larger specimens. Scanning Electron Microscope - allow scientists to view a universe too small to be seen with a light microscope. SEMs do not use light waves; they use electrons (negatively charged electrical particles) to magnify objects up to two million times. Transmission Electron Microscope - also uses electrons, but instead of scanning the surface (as with SEM's) electrons are passed through very thin specimens. Specimens may be stained with heavy metal salts.  Parts of the Microscope Parts Functions To observe specimen. Contains two or more lenses. The most common magnification for the Eyepiece eyepiece is 10X. There are also 2x and 5x. An eye piece is a removable, can be interchanged for different magnification. More than one objective lenses. These are the primary lenses of a compound microscope and can Objective Lenses have magnification of 4x, 5x, 10x, 20x, 40x, 50x and 100x. The platform below the objective lens on which the object to be viewed is placed. A hole in the Stage stage allows light beam to pass and illuminate the specimen. There are two stage clips one on each side of the stage. Once the slide containing the specimen is Stage Clips placed on the stage, the stage clips are used to hold the slide in place. It is located on the lower surface of the stage. It is used to control the amount of light that reaches Diaphragm the specimen through the hole in the stage. Simple compound microscopes have a mirror that can be moved to adjust the amount of light that Illuminator can be focused on the specimen. However, some advanced types of compound microscopes have their own light source. 2 adjustment knobs: fine adjustment & coarse adjustment knob; refine the focus of the lenses. The The Adjustments coarse adjustment knob helps in improving the focus of the low powers whereas the fine adjustment knob helps in adjusting the focus of the lenses with higher magnification. Scanning electron Transmission microscope electron microscope Magnification Your microscope has 3 magnifications: Scanning, Low and High. Each objective will have written the magnification. In addition to this, the ocular lens (eyepiece) has a magnification. The total magnification is the ocular x objective. Total magnification = magnification of eyepiece x magnification of objective lens Total Magnification Ocular lens Magnification Scanning 4x 10x 40x Low Power 10x 10x 100x High Power 40x 10x 400x  Spontaneous generation controversy A Brief History of Microbiology 1688: Francesco Redi (1626-1678) was an Italian physician who refuted the idea of Development of microscopy spontaneous generation by showing that rotting meat carefully kept from flies will not (384-322)Aristotle and others believed that living organisms could develop from spontaneously produce maggots. non-living materials. 1590: Hans and Zacharias Janssen (Dutch lens grinders) mounted two lenses in a 1836: Theodor Schwann (1810-1882) helped develop the cell tube to produce the first compound microscope. theory of living organisms, namely that all living organisms are 1660: Robert Hooke (1635-1703) published "Micrographia“; drawings and composed of one or more cells and that the cell is the basic detailed observations of biological materials made with the best compound functional unit of living organisms. microscope and illumination system of the time. 1676: Anton van Leeuwenhoek (1632-1723) 1st person to observe microorganisms. 1861: Louis Pasteur's (1822-1895) famous experiments with swan- 1883: Carl Zeiss and Ernst Abbe pioneered developments in microscopy (such as necked flasks finally proved that microorganisms do not arise by immersion lenses and apochromatic lenses which reduce chromatic aberration) spontaneous generation. exist until the present day. 1931: Ernst Ruska constructed the 1st electron microscope. Louis Pasteur's (1822-1895) famous Van Leeuwenhoek’s description of Bacteria experiments with swan-necked flasks This eventually led to: From his teeth, he observed Development of sterilization (A)& (B)- rod forms Development of aseptic technique (C) & (D)- motion pathway (E)- Spherical form (F)- Longer type of spherical form (H)- Cluster -Royal Society letter (Sept 17th, 1683) The microscope used Simple microscope (one lens)  Preparing smears for staining Staining Simple stain Differential stain Staining- coloring microbe with a dye to emphasize - staining with one stain - Uses more than one stain certain structure -mordant may be used to - Distinguish hold the stain or to coat the Gram stain specimen to enlarge it: Smear- A thin film of a microbe solution on a slide, a Acid-fast stain smear is usually fixed to attach microbes to the slide -Crystal violet, Methylene and kill microbes blue… Acid-fast stain Stained waxy cell wall is not decolorized by acid-alcohol Mycobacterium Nocardia Special stain Staining Gram stain Distinguish special parts of Distinguish Gram +ve and gram -ve Stain usually consists of +ve and –ve ion cells Capsule Gram +ve bacteria are prone Basic dye- chromophore is a cation (+ charged) to penicillin and detergents Endospore (Malachite Acidic dye- chromophore is an anion (- charged) Gram –ve are more resistant green and safranin) to antibiotics Staining the background instead of the cell is called Flagella (carbolfuchsin negative staining simple stain) Gram –ve (pink)