Outline for Microbiology
Outline for Microbiology
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Date Created: 09/25/16
BIO 120 Outline - Exam 1 1. Microscopes a. A microscope is an optical instrument that is used to observe objects so small that they cannot be seen with the naked eye. b. Resolving power is the ability to distinguish two points as separate entities. c. The magnification is the degree to which something is enlarged relative to its actual size. 2. Light Microscope a. The bright-field microscope produces a dark image against a brighter background. b. Resolution i. The resolving power of a compound light microscope is ~2 µm. ii. It is the wavelength of visible light (~4.5 µm) that limits the size of objects that can be seen. 1. If an object is less than the wavelength of light, then light will bend it around. c. If the condenser is replaced with what is known as a darkfield condenser, illuminated objects are seen against a dark background... this is known as a darkfield microscope. d. A phase-contract microscope is used to observe unstained living microorganisms. e. A differential interference contrast microscope is similar to a phase-contrast, but two beams of light are used, and a three-dimensional image is displayed. f. A fluorescent exposes a specimen under an ultraviolet light. 3. Electron Microscope a. Electron microscopes allow us to see extremely small microbes such as rabies and smallpox viruses. b. The organism has to be dead in order for us to observe it. c. They have a much higher resolving power than compound light microscopes. d. The Scanning Electron Microscope uses electrons reflected from the surface of a specimen to produce a three-dimensional image of its surface features; many SEM have a resolution of 7 µm or less. i. Displays a black and white image. 1. Eukaryotes a. Contain membrane-delimited nuclei, in other words, a true nucleus (unlike prokaryotes). i. They consist of nucleoplasm, chromosomes, and a nuclear membrane. 1. Chromosomes consist of linear DNA molecules and proteins 2. Genes are discrete units of DNA that code for a functional product. 3. Genomes are a complete set of an organism's genes. b. They also contain organelles. c. The large membrane surface area of eukaryotic cells allow greater respiratory and photosynthetic activity. 2. Eukaryotic Organelles a. Cytoplasm i. A semifluid, gelatinous, nutrient matrix that are filled with filaments called microtubules (4 to 7 nm) and actin. ii. The cytoplasm is where most metabolic reactions occur iii. They contain storage granules and a variety of organelles, while each have their own specific function. b. Endoplasmic Reticulum i. A complex set of internal membranes that may have ribosomes attached (RER), or may lack ribosomes (SER). ii. Functions include: transporting proteins, lipids, and other material within the cell; it is a major site of cell membrane synthesis; ER-associated enzymes and ribosomes synthesize lipids and many proteins. c. Golgi Complex i. Also called Golgi apparatus, Golgi body. ii. Set of membrane sacs (cisternae) that is involved in the modification, packaging, and secretion of materials. iii. Connects and communicates with the ER iv. Completes the transformation of newly synthesized proteins and packages them for storage or export. v. Creates the lipid molecules that make the membranes and vesicles of the cells. d. Lysosomes i. Lysosomes are membrane-bound vesicles that contain enzymes needed for intracellular digestion of all types of macromolecules. ii. They join with phagosomes to perform defensive tasks such as destroying any invading bacteria. e. Mitochondria i. They are nicknamed the "powerhouse" of cells. ii. ATP molecules are produced here by cellular respiration. iii. They use their own DNA and ribosomes to synthesize some of their proteins; mitochondrial DNA and mitochondrial ribosomes are similar to bacterial DNA and ribosomes in terms of size and structure... mitochondria reproduce by binary fission. f. Plastids i. Membrane-bound structures containing photosynthetic pigments. ii. They are the sites of photosynthesis. iii. Chloroplasts are a type of plastid; they contain chlorophyll. g. Cytoskeleton i. Cytoskeleton is a system of fibers throughout the cytoplasm. ii. There are three types of fibers: microfilaments, microtubules, and intermediate filaments. iii. Cell wall: 1. Some eukaryotes contain a cell wall- an eternal structure to provide shape, protection, and rigidity. 2. Chitin is found in cell walls of fungi; cellulose in cell walls of algae and plants. h. Cilia and Flagella i. Cilia and flagella are locomotor structures that differ in length and how they propel the cell. 1. Flagella are thin, whip-like organelles composed of microtubes. a. Cells containing more than one flagellum are called multiflagulated. b. Endoflagella are internal. 2. Cilia are shorter, thinner, and more numerous than flagella / "hair-like". 1. Classification of Eukaryotic Organisms a. Algae i. Characteristics and Classifications 1. Algae are photosynthetic, eukaryotic organisms. 2. All algal cells consist of cytoplasm, (usually) a cell wall, cell membrane, a nucleus, plastids, ribosomes, mitochondria, and Golgi bodies. 3. Algae range in size from unicellular organisms to large, multicellular organisms. a. Seaweed and kelp are examples. 4. Algae produce energy through photosynthesis 5. They may be arranged in colonies or strands and are found in fresh and salt water, in wet soil, and on wet rocks. 6. Depending on their photosynthetic pigments, they are classified as green, golden, brown, or red algae. 7. They include diatoms, dinoflagellates, Spirogyra, Chlamydomonas, Volvox, and Euglena. 8. Algae are important source of food, iodine, fertilizers, emulsifiers, and stabilizers and getting agents for jams and culture media. ii. Medical Significance 1. Algae secrete toxic substances called phycotoxins, which are poisonous to humans, fish, and other animals. They can lead to a disease called paralytic shellfish poisoning. b. Protozoa i. Characteristics 1. Protozoa are non-photosynthetic, unicellular, eukaryotic organisms. 2. They are found in moist environments due to a lack of cell wall; they are more animal-like than plant-like. 3. They cannot make their own food by photosynthesis, so they ingest whole algae, yeasts, bacteria, and smaller protozoa as their source of nutrients. ii. Motility 1. Protozoa usually are divided into groups and may contain flagella or cilia. c. Fungi i. Characteristics 1. They are virtually found everywhere! 2. Are nonmotile, eukaryotic cells that can be harmful or beneficial. 3. They are the major causes of plant diseases. 4. Some fungi include yeasts, molds, and fleshy fungi. 5. They are not plants... they are not photosynthetic. ii. Reproduction 1. Depending on the species, fungal cells can reproduce by budding, hyphal extension, or the formation of spores. 2. There are two types: a. Asexual – occurs by elongation of hyphae, budding, or asexual spore production. i. Asexual spores are specialized cells that are dispersed and germinate in a favorable environment to produce a new fungus; they are products of a type of cell division called mitosis. b. Sexual – occurs by producing sexual spores, which form following sexual fusion of gametes. d. Yeasts i. Eukaryotic, unicellular organisms that lack mycelia. ii. They usually reproduce by budding. iii. Some yeasts produce thick-walled, spore-like structures called Chlamydospores. iv. They can be found in soil and water and on the skins of many fruits and vegetables. v. They are used to prepare bread, wine, and beer. 1. Saccharomyces is a yeast that is used in baking. vi. Yeast colonies may be difficult to distinguish from bacterial colonies. 1. Yeasts are larger than bacteria and are usually oval-shaped. Yeasts are often observed in the process of budding. Bacteria do not bud. e. Molds i. Often seen growing in water and food. ii. They have a vegetative structure called mycelium (a multinucleate mass of cytoplasm enclosed within a system of rigid, branched, tube-like filaments called hyphae). iii. Reproduction is by spore formation, either sexually or asexually, on the aerial hyphae (mold that extend above the surface of whatever the mold is growing on). iv. Molds have great importance: 1. Some produce antibiotics, with penicillium being an example. 2. Some molds are responsible for the flavoring of some cheeses (bleu cheese, Roquefort) f. Fleshy Fungi i. Some examples are mushrooms, toadstools, puffballs, and bracket fungi. ii. They grow in soil or rotting logs. iii. Some mushrooms are edible (and can be quite delicious), while some are extremely toxic. 2. Medical Significance a. A variety of molds, yeasts, and fleshy fungi are of medical, veterinary, and agricultural importance because of the diseases that they cause in humans, animals, and plants. They are called mycoses. 1. Mycoses a. Superficial and cutaneous i. Superficial mycoses are fungal infections of the outermost areas of the human body. ii. Cutaneous mycoses are fungal infections of the living layer of the skin, the dermis. 1. A group of molds collectively referred to as dermatophytes cause tinea (ringworm) infections. 2. The yeast candida albicans can also be cutaneous, oral, and vaginal infections. b. Subcaneous and systematic i. Subcaneous and systematic mycoses are more severe. ii. Subcaneous mycoses are fungal infections of the dermis and underlying tissues. iii. Systematic mycoses are fungal infections of the internal organs of the body. iv. Inhalation of bread molds can cause disease and even death. v. Diagnosis is accomplished by culture techniques and immunodiagnostic procedure. 1. Prokaryotes b. Shape and size i. Prokaryotes are about 10 times smaller than eukaryotic cells, mainly because of their simple structure. ii. Come in a variety of shapes including spheres (cocci), rods (bacilli), ovals (coccobacilli), curved rods (vibrios), rigid helices (spirilla), and flexible helices (spirochetes) iii. All bacteria are prokaryotes or archea. c. They are reproduced through binary fission. 2. Prokaryotic Cell Membrane a. Similar in structure and function to the eukaryotic cell membrane. b. Contains a layer of a phospholipid bilayer with hydrophilic surfaces and a hydrophobic interior. c. The membrane is highly organized, asymmetric, flexible, and dynamic. d. Serves several functions: i. It retains the cytoplasm and separates the cell from its environment. ii. It serves as a selectively permeable barrier, allowing some molecules to pass into or out of the cell while preventing passage of other molecules. iii. It is the location of a variety of crucial metabolic processes including respiration, photosynthesis, lipid synthesis, and cell wall synthesis. iv. It may contain special receptor molecules that enable detection of and response to chemical in the surroundings. 3. Prokaryotic Cell Wall e. The cell wall is a rigid structure that lies just outside the plasma membrane; it provides the characteristic shapes of the various prokaryotes and protects them from osmotic lysis. i. The cell walls contain peptidoglycan, a polysaccharide polymer. ii. Gram-positive cell walls consist of a think layer of peptidoglycan and large amounts of teichoic acid. iii. Gram-negative cell walls: 1. Consist of a thin layer of peptidoglycan surrounded by an outer membrane composed of lipids, lipoproteins, and a large molecule known as lipopolysaccharide (LPS). 2. The outer membrane is more permeable than the plasma membrane because of porin proteins that form channels through which small molecules can pass. f. Glycocalyx i. Glycocalyx is a slimy, gelatinous material secreted outside the cell wall. It allows bacteria to evade the immune system. g. Flagella i. Motile bacteria possess flagella. ii. Number and arrangement of flagella are characteristic of a particular species: 1. Peritricious bacteria – flagella over entire surface 2. Lophotrichous – tuft of flagella at one end 3. Amphitrichous – one or more flagella at both ends 4. Monotrichous – single polar flagellum h. Pili (fimbrae) i. Pili are hair-like structures, most often observed in gram-negative bacteria. ii. They are composed of polymerized protein molecules called pilin. iii. Pili are thinner than flagella and have a rigid structure. iv. They enable bacteria to anchor themselves to surfaces and move through 4. Bacterial Endospores i. A few genera are capable of forming thick-walled spores as a means of survival. j. The process of spore formation is called sporulation i. They have been shown to survive for many years and are resistant to heat, cold, drying, and most chemicals. k. They are formed when bacteria face environmental stress: starvation, high temperature, antibiotics. 1. Staining a. There are three major categories of staining procedures: i. Simple ii. Structural (capsule, spore, flagella) iii. Differential (gram, acid-fast) 1. Gram Staining Procedure a. It is the most widely used differential staining procedure because it divides bacterial species into two roughly equal groups – gram positive and gram negative. i. The smear is first used with crystal violet, which stains all cells purple. ii. Iodine is used as a mordant to increase the interaction between the cells and the dye. iii. Ethanol or acetone is used to decolorize; this is the differential step because gram positive bacteria retain the crystal violet whereas the violet is washed off the gram negative, thus becoming colorless. iv. Safranin is then added as a counterstain to turn gram negative bacteria pink while leaving gram positive purple. b. Acid-fast staining can be used to identify two medically important species of bacteria – mycobacterium tuberculosis and mycobacterium leprae. i. Carbol fuschin is the red dye that is driven through the bacterial wall using heat. ii. Heat is used to soften the waxes in the cell wall. iii. Because mycobacteria are not decolorized by the acid- alcohol mixture, they are said to be acid-fast. 1. Viruses a. General Properties i. Viruses have a simple, acellular organization, consisting of one or more molecules of DNA or RNA enclosed in a coat of protein, and sometimes in more complex layers. ii. They can also be classified by size and shape, number of capsomeres (single protein unit that makes up the capsid and gives them a unique shape), presence or absence of an envelope, disease(s) they produce, target cell(s), and immunologic / antigenic properties. b. Types of Viruses i. Single stranded DNA ii. Single stranded RNA iii. Double stranded DNA iv. Double stranded RNA 2. Animal Viruses a. Classification i. Morphology – the most important characteristic for classification. ii. Physical and chemical nature are also important for classification. b. Reproduction i. There are six steps in the multiplication of animal viruses: 1. Attachment a. Viruses attach to specific receptor sites; usually cell surface glycoproteins that are required by the cell for normal cell functioning b. Viral surface glycoprotiens and/or enzymes may mediate virus attachment to the cellular receptor molecules. 2. Penetration a. There are three modes of entry: i. Changes in capsid structure leads to entry of nucleic acid into host. ii. Fusion of viral envelope with the host cytoplasmic membrane results in deposition of the nucleocapsid core within the cell. iii. Engulfment of virus within coated vesicles; lysosmal enzymes, and low endosomal pH often trigger the uncoating process. b. Once in the cytoplasm, the nucleic acid may function while still attached to the capsid components or may only after completion of uncoating. 3. Uncoating 4. Biosynthesis a. Capsid proteins are synthesized by host cell ribosomes under the direction of viral late genes. 5. Assembly a. Empty procapsids are produced. b. Nucleic acid is inserted. c. Enveloped virus nucleocapsids are assembled similarly (except for poxvirus nucleocapsids, which are assembled by a complex process that begins with enclosure of some of the cytoplasmic matrix by construction of a membrane, followed by movement of viral DNA into the center of the immature virus). 6. Escape a. Viruses escape when the host cell lyses. b. They are released by the following mechanisms: i. Virus-encoded proteins are incorporated into plasma membrane (some viruses use nuclear membrane, ER, Golgi complex, or other membranes). ii. Nucleocapsid buds outward, forming the envelope during release. 3. Latency a. Latent infections – virus stops reproducing and remains dormant for a period before becoming active again; during latency, no symptoms, antibodies, or viruses are detectable. i. Herpes is an example. 1. Once it is acquired, it never goes away. 2. Chicken pox may be followed, years later, by shingles – both result from the same virus. 4. Antiviral Agents a. Antiviral agents are drugs that are used to treat viral infections. b. Antibiotics are not effective against viral infections. c. These agents interfere with virus-specific enzymes and virus production by disrupting critical phases in viral multiplication or inhibiting synthesis of viral DNA, RNA, or proteins. d. Difficult for target viruses and antivirals often have side effects. 5. Human Immunodeficiency Virus (HIV) a. Acquired immunodeficiency syndrome (AIDS) b. It is an enveloped, single-stranded RNA virus c. Primary targets for HIV are CD4+. i. T-cells with CD4 receptors on their surface 6. Viruses and Cancer a. Oncogenic viruses (oncoviruses) cause cancer. b. Cancer-a disease where there is abnormal cell growth (neoplasia) and the spread of the abnormal cells throughout the body i. Tumor-a growth or lump of tissue; can be benign (non-spreading) or malignant (cancerous) ii. Carcinogenesis is a complex, multistep process that involves a triggering event and the activity of oncogenes. c. Vital etiology of human cancers is difficult to establish because Kochis postulates can only be satisfied for these diseases by experimenting on humans. d. Virus and human cancers i. Epstein-Barr virus (EBV) - a herpesvirus that may cause: 1. Burkittís lymphoma; found mostly in central and western Africa 2. Nasopharyngeal carcinoma; found in southeast Asia 3. Infectious mononucleosis; found in the rest of the world 4. Evidence suggests that host infection with malaria is necessary for EBV to cause Burkittís lymphoma; this is supported by the low incidence of Burkittís lymphoma in the U.S. where there is almost no malaria. ii. Hepatitis Bvirus may be associated with one form of liver cancer. iii. Human papillomavirus has been linked to cervical cancer. iv. Human T-cell lymphotropic viruses are associated with adult T-cell leukemia and hairy-cell leukemia, respectively. e. Viruses may cause cancer by a variety of mechanisms i. Viruses may carry one or more cancer-causing genes (oncogenesis). ii. Viruses may produce a regulatory protein, which activates cell division. iii. Viruses may insert a promoter or enhancer next to a cellular oncogene (an unexpressed cellular gene that regulates cell growth and reproduction), causing an abnormal expression of this gene and thereby deregulating cell growth. 7. Viroids and Prions a. Viroids i. Circular ssRNA molecules ii. No capsids iii. Cause diseases in plants iv. Do not act as mRNAs v. Mechanism that produces symptoms of disease is unknown vi. May give rise to latent infections b. Prions i. Proteinaceous infectious particles (PrP) that are not associated with a nucleic acid. ii. Genes have been identified in normal animal tissue that encode PrP 1. It is hypothesized that abnormal PrP causes prion diseases by including a change from the normal conformation of the cellular PrP to the abnormal form b. This new PrP then causes other normal cellular PrP molecules to change to the abnormal form. iii. They cause progressive, degenerative CNS disorders. 1. Bovine spongiform encephalopathy (mad cow disease) is an example.
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