Adding the class. Prerequisites. Welcome to Bio 139 General Microbiology. Syllabus. Amy Rogers, M.D., Ph.D.

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1 Adding the class Welcome to Bio 139 General Microbiology Amy Rogers, M.D., Ph.D. Lectures MW 12:00-1:15 PM (section 8) Labs: MW 1:30-2:45 PM or MW 3:00 PM-4:15 PM I anticipate a large number of students trying to add 139. Please write your name, year, & best contact info ( or phone) on sheet in front. Priority: 1. Graduating seniors 2. Other seniors; then juniors, sophomores 3. Open university Prerequisites General biology & organic chemistry Bio 10 or 20 Chem 6B, 20, or 24 If you are enrolled but lack this preparation, I will administratively drop you Exception: BioSci majors may concurrently take this class and Chem 20 or 24 upon request (talk to me or ) Syllabus Best to contact me by rogersa@csus.edu Regular office hour: Wed. 9:00-10:00 Not a good time for you? ASK me!!! MW anytime between 8:30 and 10:30 will usually work for me Textbook, lab manual, 4 Scantron 882 forms for the four lecture exams If you think you might drop, make up your mind ASAP and let me know! Do not fall behind. Pay close attention to both lecture & lab schedules for the many exam days Do not cram. 1 lecture ~~ 6 hours study Get to know my website! PowerPoint printouts of all lectures Weekly news article assignment Exam review sheets & other handouts, problem sets Book assignment Makeup exam policy: Contact me that day. Through the testing center. Chemistry quiz: Wed. September 13 th Prepare on your own: read chapter 2; see Ch.2 review PowerPoint at my website Scope & History of Microbiology, or WHAT AM I DOING HERE? Understanding microbiology is crucial to virtually all disciplines within the life sciences 1.Fundamental processes of all life {metabolism, genetics, evolution } 2.Ecology {nitrogen cycle, decomposition, deep hot biosphere} 3. Medical microbiology {although very few microbes are pathogens} 4. Food & industry {dairy, animal husbandry, biotechnology } 1

2 Applications Food microbiology fermentation, leavening, pickling; microbes as a food source MICROBES EXIST EVERYWHERE Soil Industrial Bioremediation, biosynthesis Source of antibiotics & other useful products Air Tongue Research Microbes are the workhorses of molecular biology Mass of bacteria on Earth greatly exceeds the total weight of all other living things 1. Fungi 2. Protozoa 3. Algae 4. Bacteria 5. Viruses Microorganisms: Who are they? Eukaryote Eukaryote Eukaryote Prokaryote Acellular Single-celled (Yeasts) Multi-cellular (Molds) Eukaryotic Fungi (singular: fungus) Widely distributed in water and soil as decomposers of dead organisms Some structures are not microscopic Some are important in medicine Eukaryotes: have nuclei & other organelles; generally bigger & more complex than prokaryotes Fruiting bodies (mushrooms) Fungi Mold: hyphae & conidia Fungi: Budding Yeast Macroscopic structures Microscopic 85 X 6,160 X Note scars on the right, representing sites of previous budding 2

3 Protists 1: Protozoa (singular: protozoan) Amoeba (183X) Single-celled Eukaryotic Found in a variety of water and soil environments Examples: Giardia, Leishmania, Plasmodium (malaria), Paramecium Protists 2: Algae (singular: alga) (paramecium swimming) (amoeba moving with pseudopodia) Single-celled Eukaryotic Photosynthetic Fresh water and marine environments Examples: Diatoms, dinoflagellates Micrasteria (334X) Bacteria (singular: bacterium) Single-celled Prokaryotes Major shapes: 1. Spherical cocci (one coccus) 2. Rod bacilli (one bacillus) 3. Spiral 3

4 Klebsiella pneumoniae (5,821X) Viruses Acellular entities too small to be seen with a light microscope Visible with electron microscopy Composed of nucleic acid and protein Obligate intracellular parasites Can only reproduce inside a living cell Every cell type (including bacteria) has specific kinds of viruses that can infect it Bacteriophages (35,500x) History of Microbiology Endless variety of plagues through human history {see book choice Plagues & Peoples} Black Death (bubonic plague): London, 1660 s Smallpox in the New World The Great Influenza of 1918 {see book choice Flu} But where did such sudden, massive death come from? An unseen world Anton van Leeuwenhoek Late 1600 s Dutch merchant & amateur lens grinder Best magnifications ever used (300x) First person to SEE the microbial world animalcules 4

5 Chapter 3: Microscopy Light Microscopes Specimen observed using visible light Leeuwenhoek: single lens problems with focus, various distortions Compound Light Microscope: has multiple lenses (e.g., objective & ocular lenses) Objective lens actually contains multiple lenses that correct aberrations of color & focus Light Microscopy Resolution: ability to see two things as two things (instead of one blurry thing) Iris diaphragm Resolved Not resolved (same magnification) is closely related to Long wavelength Wavelength Short wavelength Same magnification, Different resolution 5

6 Once you ve reached about 1000X magnification with a light microscope, increasing the magnification will not give you a better image: resolution is limited by the wavelength of visible light. To get clear images at higher magnification, you must use a shorter wavelength: electron microscopes Refraction Light bends when it passes from one medium to another of different optical density (different index of refraction) Ex. Water vs Air Using a light microscope: Immersion Oil Microscope specimen is on a glass slide. Light passes through glass slide air lens gets refracted At high magnification, this refraction (bending) of the light blurs the image To eliminate refraction between slide and lens: Eliminate the air, replace with immersion oil (has same index of refraction as glass) Light microscopy Problem: Most microbes are basically tiny bags of water No color, poor contrast, difficult to see Can stain the specimen This usually means the specimen must be dead Or use special types of light microscopy: Dark field, phase contrast, fluorescence Dark-field Microscopy Regular light microscopy: bright field Dark field: light does not pass through the specimen, but is reflected off it Saccharomyces cerevisiae (yeast) 975X Phase contrast microscopy A type of light microscopy particularly useful for observing live organisms Lenses enhance small differences in the index of refraction of various cell structures Perceived as different degrees of brightness 6

7 Fluorescence microscopy Ultraviolet (UV) light illuminates the specimen and excites certain molecules to emit brilliant colors (fluoresce) Some microbes fluoresce naturally Usually, microbes are stained with fluorescent dyes Commonly used to identify organisms Yeast (stained) Electron Microscopy Beam of electrons instead of a beam of light Focus using electromagnets, not glass lenses Large, expensive, difficult to use FANTASTIC magnification (up to 500,000x) and resolving power Two types: Transmission (TEM) & Scanning (SEM) Transmission Electron Microscopy Excellent for viewing internal cell structures, and viruses Specimen preparation is complex Embedded in plastic, cut into ultrathin sections (slices) with a diamond knife Scanning Electron Microscopy Excellent for viewing cell surfaces in 3D Specimen is coated with a thin layer of heavy metal such as gold, which scatters electrons TEM 67,000x SEM 40,000x Both images show E. coli bacteria Relevant chapters in Black s Microbiology: Chapter 1: Overview & History Chapter 3: Microscopy Course syllabus 7