Microbiology 290 Lecture Slides PDF

WELCOME TO MICROBIOLOGY 290!!!! Course Learning Objective (CLO) CLO 1: Compare and contrast the cellular characteristics of the various prokaryotic and eukaryotic microorganisms (including helminths) CLO 2: Describe the molecular and structural components of viruses Guiding questions...

WELCOME TO MICROBIOLOGY 290!!!! Course Learning Objective (CLO) CLO 1: Compare and contrast the cellular characteristics of the various prokaryotic and eukaryotic microorganisms (including helminths) CLO 2: Describe the molecular and structural components of viruses Guiding questions for this week: What is the correlation between Microbiology and public health? What are the basic characteristics of prokaryotes and eukaryotes? How do we classify and name microbes? How was the theory of spontaneous generation a hindrance to the advancement of the field of Microbiology? How did the debate on spontaneous generation lead to the development of the scientific method? What is Microbiology??? This is the biological study of organisms on the microscopic level. These organisms cannot be detected with the naked/unaided eye. Can be seen with the use of microscopes Microbiology is a multidisciplinary field. Parasitology Virology Bacteriology Mycology Microbiology Definition of Public Health The science and art of preventing diseases, ailments and detrimental health conditions and prolonging life. This is done through health education and health promotion. Medicine is based on cure, public health is based on prevention. Implementation of Microbiology in Public Health Most illnesses are caused by microorganisms. The study of these microorganisms can help combat them. Laboratory test is used to study these organisms. Samples of a patient’s body fluid are tested to determine whether the cause of their ailments are results of bacteria, viruses, nematodes, fungi etc. Implementation of Microbiology in Public Health Microbiology finds its way into public health in the study of food poisoning cases for individuals affected by gastrointestinal ailments. Mild forms of microorganisms are intravenously placed in the body to induce immunity as in the case of smallpox, measles, poliomyelitis and yellow fever. This is used in vaccination, one of the most important aspects of Public Health.  The Early Years of Microbiology began as a scientific Microbiology discipline in which two questions were asked: What Does Life Really Look Like? How Can Microbes Be Classified? What Does Life Really Look Like? – Antoni van Leeuwenhoek Began making and using simple microscopes Often made a new microscope for each specimen Examined water and visualized tiny animals, fungi, algae, and single-celled protozoa. Referred to these organisms as "animalcules“ and “beasties” Figure 1.3 The microbial world. Figure 1.2 Reproduction of Leeuwenhoek's microscope. Reported his findings to the Royal Society: “…Among these there were very many little animalcules, some were round, while others a bit bigger consisted of an oval…..” By end of 19th century, these organisms were called microorganisms; now they are also called microbes How do we name and classify organisms? Classification of Taxonomy is the science of classifying and naming organisms Microorganisms Biologists classify organisms for several reasons: 1. to bring a sense of order and organization to the variety and diversity of living things, to enhance communication, 2. to make predictions about the structure and function of similar organisms, and 3. to uncover and understand potential evolutionary connections.  The field of taxonomy consists of: Classification - assigning organisms to taxa Classification & based upon similarities Nomenclature - the rules of naming organisms Identification of Identification - the practical science of Microorganisms determining that an isolated individual or population belongs to a particular taxon. All members of any given taxon share certain common features which enables scientists to both organize large amounts of information about organisms and make predictions based on knowledge of similar organisms.  Linnaeus assigned each species a descriptive name consisting of its genus name and a specific epithet. Rules of Bionomial Nomenclature: Requires all taxa to have Latin or “Latinized” names (language of Science) Classifying Genus name is always a noun, and it is written first and capitalized. Organisms The specific epithet always contains only lowercase letters and is usually an adjective. Both names are either printed in italics or underlined. Because the Linnaean system assigns two names to every organism, it is said to use binomial nomenclature. Examples of Binomials: Enterococcus faecalis, a fecal bacterium. Enterococcus faecium, is in the same genus, but is a different species because of certain differing characteristics, so it is given a different specific epithet. Homo sapiens (humans); the genus name means “man” and the specific epithet means “wise.” Escherichia coli (E. coli) Full binomial must always be written before abbreviation Carl Woese Carl Woese developed the 3 domain classification system in 1970 1. Archaea 2. Bacteria Includes All Prokaryotes 3. Eukarya: Includes All Eurkaryotes Based upon analyzing the rRNA nucleotide sequences of various microorganisms This system is currently favored by microbiologists.  Modern Classification System The Taxonomic Classification System has been modified several times since Linneaus’ first system There are now 8 levels (taxa) in the Linnaean taxonomic ranking scheme Notice that higher taxonomic categories are more inclusive than lower ones.  Classification & Identification of Microorganisms Levels in a Linnaean taxonomic ranking scheme: Illustrated here are the taxonomic categories for the deer tick, Ixodes dammini, the primary vector of Lyme disease. Notice that higher taxonomic categories are more inclusive than lower ones. To simplify the diagram, only selected classification possibilities are shown (highlighted in yellow) – Figure 4.22 in textbook Classification of Viruses Viruses are not included in the 3 Domain System Are not composed of cells and are thus not considered to be a “living” organism – Must inhabit a host cell in order to replicate Although not included in the 3 Domain classification system, animal viruses are categorized on the basis of their – Genome: DNA or RNA – Viral capsid structure – Presence or absence of a viral envelope  The Exception… The only type of microbe NOT described by Leeuwenhoek are viruses – Due to their extremely small size Viruses cannot be seen via simple light microscopy – The simple technology during Leeuwenhoek’s time did not permit for the viewing of these organisms How scientists classify organisms today…. All living organisms can be sorted into one of two groups depending on the their cell structure. These two groups are prokaryotes and eukaryotes. All cells have several basic features: They are all bound by a thin plasma membrane. All cells have DNA and ribosomes, tiny structures that build proteins. How scientists classify organisms today…. All living organisms can be sorted into one of two groups depending on the their cell structure. Prokaryotes Eukaryotes Do not have membrane – Have membrane surrounding surrounding their DNA; their DNA; have a nucleus lack a nucleus – Have internal membrane- bound organelles Lack various internal structures bound with vs – Are larger, 10-100 µm in phospholipid membranes diameter – Have more complex structure Are small, ~1.0 µm in – Composed of algae, protozoa, diameter fungi, animals, and plants Have a simple structure Composed of bacteria and archaea vs COMPARISON OF EURKARYOTIC CELLS: ALGAE, FUNGI, & PROTOZOA Figure 1.4 Cells of the bacterium Streptococcus (dark blue) and two human cheek cells. Prokaryotic Nucleus of bacterial cells eukaryotic cheek cell Figure 1.8 An immature stage of a parasitic worm in blood. Red blood cell Figure 1.9 A colorized electron microscope image of viruses infecting a bacterium. Virus Bacterium Viruses assembling inside cell WEEK 1: LECTURE VIDEO 3 CONTENT  The Golden Age of Scientists searched for answers Microbiology to four questions – Is spontaneous generation of microbial life possible? – What causes fermentation? – What causes disease? – How can we prevent infection and disease?  CONTROVERSY: In the fourth century B.C., the Greek philosopher and scientist Aristotle argued that some living things can arise suddenly, from inanimate matter, without the need for a living progenitor to give them life. Spontaneous He thus proposed the theory of Spontaneous Generation Generation which stated: “Living things can arise from nonliving matter” Debate Process is also referred to as abiogenesis Some philosophers and scientists of the past thought living things arose from one of three processes: – Asexual reproduction – Sexual reproduction with copulation – Sexual reproduction without copulation After Aristotle’s proposal, it was believed that spontaneous generation was the fourth means of reproduction  Spontaneous generation finally came under challenge in the 17th century Some in the scientific community began to Spontaneous doubt its validity Generation Was finally proven that spontaneous generation Debate was an incorrect hypothesis AND that nonliving things are NOT capable of producing life. The work of four major scientists are noted  John Needham – British investigator – Supported Aristotle’s theory of spontaneous generation Needham’s Experiments – Boiled beef gravy and infusions of plant material in vials, which then placed with vials tightly sealed with corks – Several days later, he observed that the vials were cloudy (indication of microbial growth) – Via examination of the infusions, he noticed an abundance of “microscopical animals of most dimensions” http://www.slideshare.net/franklc/scope-and-history-of-microbiology  Conclusion – Needham’s rationale was that since he’d heated the vials to sufficiently kill everything, the growth had to be due to spontaneous generation – Twenty years later these results were refuted by Spallanzani  Experiments of Lazzaro – Refuted Aristotle’s theory Spallanzani of spontaneous generation – Conducted experiments which contradicted Needham’s results Spallanzani’s Experiments – Boiled gravy infusions for almost an hour and sealed the vials by melting their slender necks closed – His infusions remained clear unless he broke the seal and exposed the infusion to air (in which event they did become cloudy) http://image.slidesharecdn.com/fbiologysimplepplessonbiologyscientific-method-090401222242-phpapp01/95/biology-scientific- method-11-728.jpg?cb=1238624603 Conclusion – Spallanzani concluded that: Needham failed to heat vials sufficiently to kill all microbes or had not sealed vials tightly enough Microorganisms exist in air and can contaminate experiments Spontaneous generation of microorganisms does not occur Experiments of Louis Pasteur Louis Pasteur – French chemist also known as the “Father of Microbiology” – Refuted Aristotle’s theory of spontaneous generation – Conducted experiments which supported Spallanzani’s results – His experiments disproved and finally ended the controversy surrounding spontaneous generation Boiled infusions long enough to kill everything, but instead of sealing the flasks, he bent their necks into an S-shape, which allowed air to enter while preventing the introduction of dust and microbes into the broth Experiments of Louis When the “swan-necked flasks” remained upright, no microbial growth appeared Pasteur When the flask was tilted, dust from the bend in the neck seeped back into the flask and made the infusion cloudy with microbes within a day Experiments of Louis Pasteur  The Scientific Debate over spontaneous generation led in part to development of scientific method Method – – Observation leads to question Question generates hypothesis – Hypothesis is tested through experiment(s) – Results prove or disprove hypothesis Accepted hypothesis can lead to theory/law Disproved hypothesis is rejected or modified Figure 1.13 The scientific method, which forms a framework for scientific research. WEEK 1: LECTURE VIDEO 4 CONTENT  The Golden Age of What Causes Fermentation? Microbiology – Spoiled wine threatened livelihood of vintners – Some believed air caused fermentation; others insisted living organisms caused fermentation – Vintners funded research of methods to promote production of alcohol and prevent spoilage during fermentation – This debate also linked to debate over spontaneous generation Figure 1.14 How Pasteur applied the scientific method in investigating the nature of fermentation. What Causes Fermentation? – Pasteur's experiments Led to the development of pasteurization – Process of heating liquids just enough to kill most bacteria Began the field of industrial microbiology – Intentional use of microbes for manufacturing products Pasteur developed Germ Theory of Disease – Some diseases were caused by an infectious agent or ‘germ’ What Causes Disease? – Robert Koch studied disease causation (etiology) Anthrax Examined colonies of microorganisms Developed Koch’s Postulates – still used today to establish the link between a particular microorganism and a particular disease What causes disease: Koch’s Postulates and TB 50 What Causes Gram-negative Gram-positive Disease? Developed by Hans Christian Gram Distinguishes between bacteria based upon cell wall traits Divides bacteria into 2 groups: Gram + and Gram - Figure 1.17 Results of Gram staining.  How Can We Prevent Many great advances in disease prevention came after it was shown that microbes can Infection and cause disease Modern principles of hygiene not widely practiced in the mid-1800s Disease? Healthcare associated infections were common Six health care practitioners were instrumental in changing health care delivery methods The Golden Age of Microbiology How Can We Prevent Infection and Disease? – Semmelweis and handwashing Ignaz Semmelweis required medical students to wash their hands in chlorinated lime water Resulted in higher patient survival rates – Lister's antiseptic technique Joseph Lister advanced antisepsis in health care settings Sprayed wounds, surgical incisions, and dressings with carbolic acid (phenol) How Can We Prevent Infection and Disease? – Jenner's vaccine – Ehrlich's "magic bullets" Edward Jenner developed a vaccine Paul Ehrlich worked to identify "magic against smallpox bullets" that would destroy pathogens but Demonstrated the validity of vaccination not harm humans Began the field of immunology Discoveries began the field of chemotherapy The Modern Age of How Do We Defend Against Disease? – Serology Microbiology The study of blood serum Von Behring and Kitasato – presence in the blood of chemicals and cells that fight infection – Immunology The study of the body's defenses against specific pathogens – Chemotherapy Fleming discovered penicillin Domagk discovered sulfa drugs The Modern Age of Microbiology What Role Do Microorganisms Play in the Environment? – Bioremediation uses living bacteria, fungi, and algae to detoxify polluted environments – Recycling of chemicals such as carbon, nitrogen, and sulfur – Most microbes in the environment are not pathogenic The Modern Age of Microbiology What Will the Future Hold? – Microbiology is built on asking and answering questions – The more questions we answer, the more questions we have The Modern Age of Microbiology What Are the Basic Chemical Reactions of Life? – Biochemistry Began with Pasteur’s work on fermentation and Buchner’s discovery of enzymes in yeast extract Kluyver and van Niel—microbes used as model systems for biochemical reactions Practical applications: – Design of herbicides and pesticides – Diagnosis of illnesses and monitoring of patients’ responses to treatment – Treatment of metabolic diseases – Drug design Figure 1.20 The effects of penicillin on a bacterial “lawn” in a Petri dish. The Modern Age of Microbiology How Do Genes Work? – Microbial genetics – Molecular biology – Recombinant DNA technology – Gene therapy The Modern Age of Microbiology How Do Genes Work? – Microbial genetics Avery, MacLeod, and McCarty determined genes are contained in molecules of DNA. Beadle and Tatum established that a gene’s activity is related to protein function. Translation of genetic information into protein explained Rates and mechanisms of genetic mutation investigated Identify methods cells use to control genetic expression The Modern Age of Microbiology How Do Genes Work? – Molecular biology Explanation of cell function at the molecular level Pauling proposed that gene sequences could: – Provide understanding of evolutionary relationships and processes – Establish taxonomic categories to reflect these relationships – Identify existence of microbes that have never been cultured Woese and Fox determined cells can be categorized as bacteria, archaea, or eukaryotes. Cat scratch disease caused by unculturable organism The Modern Age of Microbiology How Do Genes Work? – Recombinant DNA technology Genes in microbes, plants, and animals manipulated for practical applications Production of human blood-clotting factor by E. coli to aid hemophiliacs – Gene therapy Inserting a missing gene or repairing a defective one in humans by inserting desired gene into host cells The Modern Age of Microbiology What Role Do Microorganisms Play in the Environment? – Bioremediation uses living bacteria, fungi, and algae to detoxify polluted environments. – Recycling of chemicals such as carbon, nitrogen, and sulfur – Causation of disease Where to Find Your Assignments HOMEWORK  Discussion Forums Reminder Discussion posts must be completed Each week, you are required to submit The required posts per initial prompt during the week they are assigned. a reply to each initial prompt and are described as follows: Discussion posts made in advance of replies to your peers or instructors in No later than Wednesday, 11:59 p.m. the assigned week will not count the Discussion Board. An automatic (Pacific time) each week, you must toward the weekly discussion grade. If 10% point deduction will be assessed post one (1) response to each initial you wish to work ahead, please for all late initial postings. prompt posted by the instructor compose your responses in a Word throughout the week, and no later than document, then post when the week the conclusion of each week, you must arrives. Note: There may be more than one initial prompt per week, depending on reply to a minimum of two (2) peers the course and material covered. It is and/or instructors, per initial prompt, your responsibility to reply accordingly. although replying to more is highly encouraged. Replies must be made throughout the week to show active participation. Looking In this lecture, we covered the majority of Chapter 1 and portions of Chapters 3 and 4 Ahead You are responsible for knowing the content covered in the lecture videos from these assigned chapters. Do NOT depend solely on the PowerPoint. Read more about this content in the above stated Chapters. In Week 2, we will go more in depth in covering Chapter 3. Read this chapter as well as the portion of Chapter 24 that pertains to Gonorrhea and Syphilis. Assignments due next week – Homework: Week 1-1 (access via the Assignments link on Mastreing) – Week 1 and Week 2 Discussion forum: Due by Sunday night at 11:59 pm for Sections 1A, 1B and 1C (Monday lecture session)