BIOL220 General Microbiology Course Overview PDF

Welcome to BIOL220 General Microbiology Your Instructors Primary Dr. Zach Burcham Instructor [email protected] OH: Wednesday 1:45-2:45pm; SERF 601 or by appointment Teaching Madison Criswell Assistant [email protected] OH: Tuesday 12-1pm; Mossman 5th floor lobby Biology Degree Learning Objectives...

Welcome to BIOL220 General Microbiology Your Instructors Primary Dr. Zach Burcham Instructor [email protected] OH: Wednesday 1:45-2:45pm; SERF 601 or by appointment Teaching Madison Criswell Assistant [email protected] OH: Tuesday 12-1pm; Mossman 5th floor lobby Biology Degree Learning Objectives This course satisfies a requirement within the Biological Sciences degree curriculum. As such, we strive to explain the five big ideas (FBIs) in biology as they relate to microbiology. 1. Evolution 2. Structure and Function 3. Information Flow and Storage 4. Transformations of Energy and Matter 5. Systems We will be covering an extremely broad range of topics. Hopefully, you find something interesting to you! How to succeed in this class PDF of Powerpoint slides will be posted to canvas prior to each lecture Read the assigned textbook sections Attend class every day Get help as soon as something isn’t clear! Office hours are a free resource! Study in advance of exams… don’t “cram”. NO STUDY GUIDES, PRACTICE EXAMS, ETC. They aren’t necessary! You will be given all lecture and synthesis day slides We will have synthesis and review days Review days are a targeted and concise revist of previous material Schedule Quick Peak Full schedule on Canvas and subject to change Reading Quiz 1 and 2 DUE Exam review the class before the exam 1.1-1.5 In the event of leaking issues, we will transition to recorded/zoom lectures until it is fixed. 1.1-1.5 Support for Learning Microbiology: An Evolving Science, 6th ed. Slonczewski JL, Foster JW, Zinser ER. W. W. Norton & Co. The Hardcopy version of this textbook is available from the UT Bookstore. The link to the eBook can also be accessed through Canvas under Modules Canvas to Access Course Materials Lectures will be posted before class but some content can change Lectures will NOT be recorded* Assignment materials posted online Timed reading quizzes on Canvas Course Grading Components of your grade: 4 exams, each worth 100 points Online Canvas reading quizzes, totaling 100 points Clicker questions / Attendance, totaling a max of 50 points Semester project, totaling 100 points Be aware that Absolutely No Extra Credit will be available for this class. Exams (4 in Total) Consist of approximately 70% multiple choice and 30% fill in the blank, and short thought questions. The use of review sheets and electronic devices are strictly prohibited during exams. The Final Exam will be not be cumulative Exam questions will be solely based on the materials discussed in class. Some questions will require that you answer in complete sentences. If we cover it in class, synthesis day, and review day then you will almost certainly see it again! TIP: Create your own practice exam from review days, synthesis days, and lectures Reading Quizzes There will be 13 timed, online quizzes offered through Canvas, each worth 10 points. The 10 best scores will make up your final quiz grade. They will be made available 1 week in advance and will be due by class time The first and second quiz will be due Feb. 5th due to textbook access issues These are reading quizzes that cover the lecture sections for the coming week. The goal is for the lecture to NOT be the first time you see material. Clicker Questions EVERYDAY we will have 2-4 in-class, multiple choice questions. If you get an answer correct it will contribute 1 point towards your clicker-based quiz point total. If you get an answer incorrect it will contribute 0.5 points towards your clicker question point total. The MAXIMUM number of Clicker-based question points you can earn that will be applied towards your final grade is 50 points. We will offer somewhere between 60-70 points. THERE ARE MORE POINTS AVAILABLE THAN YOU CAN USE. NO makeup clicker-based question points. PointSolutions Clicker Questions PointSolutions app - this can be downloaded through the App Store or Google Play Store Web browser - have students open https://ttpoll.com in a web browser. They will be prompted to login and enter your session ID. SESSION ID: microbiol – Try to connect right now for test question (doesn’t count towards clicker points) Semester Project Everyone will be assigned a semester-long project to complete INDIVIDUALLY. The semester project will be introduced following Exam I. Research an approved scientist and read an approved peer-reviewed research manuscript by this scientist. Write a report on the scientists’ background, research topic/field, and contribution to that research topic followed by a discussion/interpretation of one of the selected research manuscript. The report will be 4-6 pages, double-spaced, Calibri/Arial font size 12, 1-inch margins. The semester project is worth 100 points and due April 26th by midnight through Canvas under Assignments. Final Grading Example: Johnny wants to know if he’ll be able to graduate in December, so he wants to calculate his final grade. For exams he earned 72, 75, 64 and 66 points (69.3 avg). He earned 45 points via clicker points. He earned 95 points via reading quizzes He earned 95 points via semester project. To calculate his grade Johnny adds: 72+75+64+66+45+95+95 which equals 512 points. Johnny then divides 512 by 650 to get 0.788 which equals 78.8% which results in a final grade of a B-. CHAPTER 1 Microbial Life: Origin and Discovery Copyright © 2024 by W. W. Norton & Company, Inc. Chapter Objectives (Ch 1.1 – 1.5) 1. Know the definition of microbe and discuss the contradictions that arise from the word microbe. 2. Provide examples of microbes and scientists that profoundly affected human history. 3. Understand how all life forms are categorized on the phylogenetic tree of life 4. Relate the biological diversity present among prokaryotes to that of eukaryotes. Introduction § Microbes grow almost everywhere, and they are incredibly abundant and diverse. § Evidence of microbial life dates back 3.7 BILLION years § For context, the Earth is roughly 4.5 billion years old § Most of Earth’s microbial diversity remains a mystery. 18 1.1 What Is a Microbe? § A microbe is a living organism that requires a microscope to be seen. § Some contradictions or misclassifications from this? Viruses? Protists? § Each microbe contains in its genome the capacity to reproduce Largest discovered bacterium Amoeba 19 Many Different Types of Microbes Prokaryotes: cells lacking a nucleus Eukaryotes: cells with a nucleus Viruses and prions (acellular entities) § Bacteria, archaea, and eukaryotes— known as the three “domains”— evolved from a common ancestral cell 20 Microbial Genomes § A genome comprises the total genetic information of an organism. § Understanding genomes helps us understand how microbes “work”. § Metagenomes: collections of sequences from diverse populations of microbes taken directly from the environment. Fred Sanger 21 1.2 Microbes Shape Human History Since Earliest Civilizations Yeasts and bacteria yielded beneficial fermented foods and beverages but spoiled meat and wine. “Rock-eating” bacteria aided metal mining and deteriorated ancient stone monuments. Microbes of all types caused diseases and famines. 22 Microbial Diseases Have Profoundly Affected Human Demographics and Cultural Practices Fourteenth century: bubonic plague caused by Yersinia pestis Nineteenth century: tuberculosis caused by Mycobacterium tuberculosis Today: coronavirus disease (COVID19) caused by the SARS-CoV-2 virus 23 Florence Nightingale (1820-1920) British Nurse who founded the science of medical statistics. Devised the “polar area chart.” Showed more soldiers died from infection than combat wounds. ABX wouldn't be discovered until 1928 or used until 1941 24 Robert Hooke (1635–1703) Built the first compound microscope Published Micrographia, the first manuscript that illustrated objects observed with a microscope Coined the term “cell” 25 Antonie van Leeuwenhoek (1632–1723) Built single-lens magnifiers, complete with sample holder and focus adjustment First to observe single-celled microbes – Called them animalcules meaning “small animals” 26 Spontaneous Generation: Do Microbes Have Parents? § The theory of spontaneous generation suggested that living creatures could arise without parents. § In 1660s, maggots in decaying meat were shown to be the offspring of flies. § In 1760s, a sealed flask of meat broth sterilized by boiling failed to grow microbes § But what if air is necessary for spontaneous generation? 27 Louis Pasteur (1822–1895) Discovered the microbial basis of fermentation, vaccination, and pasteurization Produced data that refuted spontaneous generation – Invented the “swan-neck” flask – Showed that a broth boiled in a swan-neck flask remained free of microbial growth, despite being exposed to air 28 29 1.3 Medical Microbiology § The germ theory of disease suggests that many diseases are caused by microbes. § Robert Koch (1843–1910) German physician Developed principles and methods crucial to microbial investigation Applied his methods to the study of several lethal diseases around the world 30 Koch’s Postulates Ordered set of criteria for establishing a causative link between an infectious agent and a disease. What could be some issues with these criteria? 31 Immunization Prevents Disease § In the eighteenth century, smallpox infected a large fraction of the European population. § Lady Mary Montagu introduced the practice of smallpox inoculation to Europe in 1717. 32 Immunization Prevents Disease § Edward Jenner (1749–1823) deliberately infected patients with material he collected from cowpox lesions. The practice of cowpox inoculation was called vaccination 33 Immunization Prevents Disease § Louis Pasteur developed the first vaccines based on attenuated (weakened) strains of microbes. § Immunization is the stimulation of an immune response by deliberate inoculation with an attenuated pathogen. 34 Antiseptics and Antibiotics § In 1847, Ignaz Semmelweis ordered doctors to wash their hands with chlorine, an antiseptic agent. 35 Antiseptics and Antibiotics § In 1929, Alexander Fleming discovered that Penicillium mold generated a substance that kills bacteria. § By 1941, Penicillin quickly became the first commercial antibiotic used to save human lives. 36 1.4 Environment and Ecology § Microbes cycle the many nutrients essential for life, including all global N2 and most of the O2 in Earth’s atmosphere. Less than 0.1% of all microbial species can be cultured 37 Sergei Winogradsky (1856–1953) Russian scientist who was among the first to study microbes in natural habitats Winogradsky column Model of a wetland ecosystem containing regions of enrichment for microbes utilizing diverse metabolisms 38 Winogradsky and others showed the importance of bacteria in geochemical cycling. 39 Microbial Endosymbiosis with Plants and Animals § Endosymbionts are microbes that live inside a larger host organism. 40 1.5 The Microbial Family Tree § Diversity of microbial life forms presented 19th-century microbiologists with a seemingly impossible task of classification 41 Microbes Are a Challenge to Classify § Early taxonomists faced two challenges as they attempted to classify microbes: 1. Resolution of the light microscope was too low. 2. Microbial species are hard to define. – Nevertheless, microbiologists have devised working definitions of microbial species. o Similarity of DNA 42 Microbes Include Eukaryotes and Prokaryotes 1. Determined microbes are neither plant nor animal 2. A third category of life, the Monera, for microbes 3. Divided Monera into two groups: 1. Eukaryotic protists 2. Prokaryotic bacteria 4. Added Fungi as a fifth kingdom of eukaryotic microbes 43 Eukaryotes Evolved through Endosymbiosis § Lynn Margulis (1938–2011) proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes. § The endosymbiosis theory was highly controversial. 44 Archaea Differ from Bacteria and Eukaryotes § In 1977, Carl Woese studied prokaryotes that live in hot springs and produce methane. § Analysis of their DNA revealed that these prokaryotes were a distinct form of life. § More closely related to eukaryotes § Woese called these new prokaryotes the archaea. 45 Woese’s discovery replaced the classification scheme of five kingdoms with three equally distinct groups called domains. The bacterial ancestor of mitochondria derives from ancient proteobacteria, whereas chloroplasts derive from ancient cyanobacteria. 46