Chapter 1: Introduction/History of Microbiology 1/9/17 https://quizlet.com/150220545/chp1scopeandhistoryofmicrobiologyflashcards/ I. Microbiology From the Greek mikros (small) , bios (life) and logos ∙ Mikros Small ∙ Bios Life ∙ Logos Depending on context, can mean “a word” or “the rational principle that governs the universe” An “ology” is the study of something II. Who it’s for: 1. Everyone in the modern US knows something about microbiology 2. Wash hands during flu season 3. We cover cough/ sneeze 4. Don’t drink off of sick people’s cups III. Why: ∙ Future healthcare professionals have the health, bodily integrity, and lives of their patients in their hands o Not just nurses, PA, or other directcare professions either 4 Dead From Rare Fungal Meningitis Charged with murder (MA) ∙ To understand a thing, you should start from beginning IV. Can/Cannot See Microbes ∙ Could not be seen before the late 1500 or early 1600s o For thousands of years, mankind could only infer from what could be seen Pains, fevers, boils, rashes and other external symptoms o The Great Ptolemaic Smackdown o Earliest evidence of the dawning of what would become microbiology is probably found in medicine, sanitation and food o First seen in drawings Salubrious Sumeria∙ Brewing of cereal beverages (beer) and baking bread has a very long history ∙ Evidence such as pictorial and cuneiform tablets from the middle East (Levant) indicate that beer brewing is at least 5000 years old ∙ The Hymn to Ninkasi (~1800 B.C) speaks of the baking of bread and brewing of beer Semitic Sanitation ∙ Oldest Western documents may show evidence of protomicrobiology o Proto From Greek word protus which means “first” o Deuteronomy 23:1213 (ESV) o Deuteronomy 23:14 (ESV) V. Chinese Counterparts ∙ Excavation started in 2004 has recently yielded evidence of ~3000 B.C. of beer brewing ∙ Both equipment and evidence of grain processing were found VI. Indian Innovation ∙ Protomicrobiology evidence can be found in ancient SouthAsia as well ∙ “It is good to keep water in copper vessels, leave it in the sunlight, and filter it through charcoal.” Translated from Sanskrit found in Sushruta Samhita, ~2000 B.C. VII. To Take the Oath ∙ Greeks weren’t left out ∙ Hippocrates of Kos (460 370 B.C.) took note of disease symptoms and realized that they might be transferred somehow by clothing or other objects ∙ Worked with theory that disease was caused by improper mixing of the four bodily humors o Yellow Bile Spleen o Black Bile Gallbladder o Phlegm Brain/lungs o Blood Liver Athenian Connection ∙ Thucydides of Athens (460400 B.C.) wrote a History of the Peloponnesian War ∙ In the summer of 430 B.C. there was a plague, possibly typhoid fever, that killed nearly 33% of the Athenian population; more than the Archidamian War (first part of the war)∙ He noted that those who had suffered from the plague and survive could care for the sick without being endangered again ∙ Believed it was Typhoid fever Roman Longevity ∙ Marcus Terentius Varro (116 27 B.C.) was an ancient roman scholar o Count him as yet another good thing ∙ Suggested that there are bred certain minute creatures which cannot be seen by the eyes and float in the air and enter the body through mouth, nose and cause serious diseases ∙ “What is sauce for the goose is sauce for the gander” VIII. Only One Left ∙ Bubonic plague was known as the “Black Death” in Europe ∙ First record that we have of an outbreak is 542 A.D. which has been called “The Plague of Justinian” o Affected the Eastern Roman empire, especially Constantinople ∙ 13% of the world’s population was killed o Current equivalent = 1 billion 250 million more people than the current population of Europe ∙ Came back in 1347 (everyone remembers) IX. Takeaways ∙ Medicine, food and sanitation are all roots for microbiology ∙ Empirical evidence was only what you could see with unaided human eye ∙ Microbes were unknown but their existence was hypothesized by some of the ancients ∙ Were not stupid ∙ Ancient systems that predate what we now call “science”, “religion”. Or “metaphysics” are essential pillars of our modern understanding History & Scope 1/11/17 Protomicrobiology in Sumeria, Sianai, Greece, India and China I. Technology ∙ Development of optical technology allowed a leap forward∙ Englishmen Robert Hooke coined the term “cell” around 1665 after observing some cork using his homemade compound microscope ∙ Contemporary in the Netherlands, Anton van Leeuwenhoek spent time observing “animalcules” (living organisms) II. Anton van Leeuwenhoek ∙ Observed and described all the major types of microorganisms i. Basic histology ii. First realized the amount of how many microorganisms in our environment iii. Took sample from mouth and vinegar ∙ Did not share technique to develop and improve microscope until he died in the 1950’s that his lens manufacturing process was rediscovered III. Germ Theory o Spontaneous generation (abiogenesis) very popular o Galan most famous in medicine and Hippocrates Miasmic (bad air) Theory o Other side: biogenesis (living things come from living things) Goes along with Germ Theory “Microorganisms cause some disease” o Took hundred years of solid results and supporting argument to get spontaneous generation back on its heels IV. Reasonable ∙ From before Aristotle (384 – 322 B.C.) until after John Needham (1713 1781 A.D.) the idea of spontaneous generation was popular ∙ Francisco Redi done experiments showing meat in jar and cover jar, flies don’t show up V. The Contest o French Academy of Sciences sponsored a competition in 1859 Two main contestants: Louis Pasteur and FelixArchimedes Pouchet o Pouchet argued that microorganisms were produced by chemical processes like fermentation and putrefaction o Pasteur argued that organisms must come from an outside source and were not spontaneously produced in situ Both were not good arguments VI. Pasteur’s Permanence∙ Past experiments made use of obstructions ∙ First Pasteur (in 1862) with his goose neck flasks ∙ Left them open to the charge that the air itself was somehow chemically altered by passing through the obstructions VII. John Tyndall (1870) ∙ Settling box: close and sit and everything would settle out of it and could make measurements with purified air i. Devised experiments that controlled for chemical air change VIII. Koch & Hess ∙ Not all budding microbiologists were mired in the biogenesis/abiogenesis debate ∙ German doctor Koch (18471910) spent a great deal of his career studying pathogenic microorganisms i. Looked at anthrax, tuberculosis, cholera and many others ii. Went to sick people and got samples and made cultures ∙ Needed to work in vitro (in glass) developing pure cultures ∙ Medicine and science are team sports ∙ Angela Hess, wife of assistant, Walter Hess, who suggested that Dr. Koch try using agarager as the basis for his solid microbiological medium i. She was a jam and jelly master ∙ Ager gave his microbiological media a firm, liquefactionresistant surface on which microorganisms would grow IX. Semmelweis & Lister ∙ Controlling infections ∙ Hugarian doctor Ignaz Phillipp Semmelweis (18181865) noticed differences between the frequency of puerperal fever (septic infection) in doctor or midwife birthing wards i. Insisted that doctors wash their hands in a chlorinated lime solution cut the mortality rate for new mothers to <1% ii. Did not have solid explanation, suggestions were largely rejected by the Austrian medical establishment ∙ Sir Joseph Lister, baronet (18271912) worked in Scotland and England. Carried Semmelweis’ work forward i. Big user of phenol for organic ii. Pioneered the use of antiseptics (mainly phenol) which led to the development of sterile surgeryiii. When his wife, who was his closets research partner died in 1893, he lost much of his love for writing and studying X. Branching Out ∙ Men and women that we have seen so far were generalists or amateurs ∙ Nuanced developments in technique are often the bailiwick of specialists (generalists) ∙ Once technology was developed, by generalists, basic principles could be founded ∙ Foundation is set, house can be built, rooms are i. Immunology ii. Virology iii. Chemotherapy iv. Genetics and Molecular Biology XI. Immunology ∙ Disease transmission isn’t only about organisms but also host response i. Thucydides noted typhoid immunity and resistance ∙ In both China & Europe people noticed the link between cowpox infection and small pox immunity ∙ Pasteur, Koch and others experiments with vaccines created using weakened or killed pathogens ∙ Englishmen Edward Jenner (17491823) was an early pioneer of such techniques ∙ Russian Ilya Ilyich Eli Mechnikov (18451916) came later and first described phagocytes. He established cellmediated immunity i. Starfish fell on floor due to child ii. Liquid came out and allowed him to see phagocytes ∙ Paul Ehrlich (18541915) developed humoral (antibody) immunity XII. Virology ∙ Came after bacteriology ∙ Development of porcelain filters capable of straining out bacterial cells led to the discovery of infectious things that could transverse them ∙ Russian Dmitri Iosifovich Ivanosky (18641920) was the first to discover viruses while studying tobacco disease in Crimea, Ukraine (findings published in 1892)∙ Dutchman Martinus Willem Beijerinck (18511931) who independently replicated the work in 1898 who coined the term virus from the Latin virus which can mean slime or poison (thought it was liquid nature) ∙ Wendell Meredith Stanley (19041971) who successfully crystalized tobacco mosaic virus in 1935 and observed particles by electron microscopy in 1939 ∙ RNA and DNA viruses were delineated in 1952 ∙ Development is ongoing XIII. Chemotherapy ∙ Many diseases or symptoms can be treated with chemicals ∙ Greek Pedanius Dioscordies (4090 A.D.) a surgeon who worked as a medic in the Roman Army i. Five volume De Materia Medica (On Medical Material) was widely read for 1500 years) 1. Described morpheine, muscle relaxers, etc Erlich ∙ First chemotherapist ∙ Early discovery that there were dyes that would stain microorganisms but not animal cells led him to search for the “magic bullet” chemical that would selectively kill microbes ∙ Coined term “chemotherapy” tested hundred of compounds against dozens of pathogenic organisms ∙ Significant commercial success with his Salvarsan, which was effective against syphilis i. Caused loss of life or limb (arsenicmediated) ∙ Erhlich prepared the way for antibiotics which were soon to come to their prime Genetics & Molecular Biology • This is the youngest branch of Microbiology. • Much research is currently being done on the genetics of microbes and what those genetics mean for the molecular biology of the cell (or virus). • This branch of microbiology began to become distinct when Austrian Gregor Mendel’s (18221884) principles of genetics were rediscovered. • Mendel should have his own slide, but it’s a bit off topic. For a fascinating read, see The OFloinn’s De evolutione evolutionis. • The rediscovery (or rather, wide dissemination) of Mendel’s work on biological inheritance answered many vexing questions about microbial characteristics.• From this branch of microbiology has sprung AIDS research, gene therapy, genetic modification of plants, designer bacteria, and many other modern marvels. It’s Not All Medicine • Microbes are believed to make up ~60% of the Earth’s biomass. • They do a lot more than just cause diseases. • There are microbes on your skin that protect you from infection. • There are microbes in your digestive tract that produce vitamins for you. • There are microbes that run nutrient cycles in the environment. • Most of the oxygen in the atmosphere is fixed by microbes. Takeaways from Lecture 2 • Big things start small. • Great discoveries often come from screwups. • Science, medicine, and all other worthy pursuits are team sports. • A large ego may get you into the history books but it will often impede the development of interesting and lifesaving techniques and technology. • All human goods come from concern (love) for your neighbor. Supplemental Slides The Bacteria • Bacteria is plural. Bacterium is singular. • From the Greek bakterion which means “little stick”. • Domain: Bacteria. • Most are distinctly singlecelled. • Most have a definable rod, spherical, or spiral shape. • Some are filamentous. • Almost all require the highest magnification if viewed with a light microscope. • They have no nucleus or other membranebound organelles. • Most or heterotrophic. • Many can swim. • They have been found in every environment that man has accessed on Earth. The Archaea • From the Greek archaîos meaning “ancient”. • Similar bacteria in form and appearance.• Domain: Archea. • Also singlecelled, no nucleus. • Very different metabolism, genetics, cell walls, and flagella. • Most have been found in extreme environments. • Are not currently known to cause disease but… • Have be found in the digestive tract of some ruminants. The Algae • Singular alga. • From Latin alga “seaweed” first known use in 1550’s. • Most are singlecelled. • Some marine algae can be quite large and multicellular. • Domain Eukarya, for the most part. • Nuclii, membranous organelles, generally photosynthetic. • Not ALL are, contrary to what the book says. • Many can move and they are found in virtually all sunlit aquatic environments. • In Columbia, this can include your siding. • Very few directly cause disease in humans. • Prototheca can cause mastitis in dairy cows. • Karenia brevis can bloom and cause red tides. • Dinoflaggelates/cyanobacteria may produce Saxitoxin which concentrates in shellfish and can sicken or kill. The Fungi • Singular fungus. • From Latin, literally, “a mushroom”. • Domain Eukarya. • Includes yeasts, molds, mushrooms, etc. • Generally heterotrophic. • Immobile but perhaps with extensive networks of hyphae. • Common in freshwater and soil as decomposers. • Some cause disease, others produce antibiotics, some are just plain delicious. The Viruses • Remember the word origin? • Acellular. • Domain: NONE. • Require electron or Xray microscopy to view. • Packets of a few very specific proteins and nucleic acids.• Can be crystalized like proteins, nucleic acids, or minerals. • Only appear living when they have coopted a living cell. • Related: viroids and prions. The Protozoa • Singular protozoan. • A compound from the Greek proto (first) and zoion (animal). • Domain Eukarya. • Singlecelled, generally microscopic. • Most, except for human parasites, are locomotive. • Many are phagocytizers. • Common in soil, water, and some animal vectors. The Helminths & Arthropods • Not technically microbes but some have human health importance. • Helminth comes from the Greek helmins “parasitic worm”. • Some helminth life stages are human parasites. • Arthropod, also Greek, arthron “joint” and podus “footed”. • Very large Phylum including many things from terrestrial insects to lobsters. • Some insects are disease vectors, sometimes carrying helminths. Applied Microbiology (Chapter 26) 1/13/17 EXAM People of past What they did Timeline of people Date of first black death: 542 A.D. Mr. Sterner’s article Picture Avicenna ∙ Monument Mausoleum in Hamadan, Iran ∙ On stamps mostly 1980 Microbiology has always been “applied” Detail from TT52, The Tomb of Nakht, scribe and serving priest of the Eighteenth Dynasty (15431292 BC) and his wife Tawy, chantress of Amon Making wine (applying microbiology) L’Exaltation de la Fleur (470460 BC); bas relief. Currently located in the Louvre Discussion flowers, fungi, mushrooms, bones? Bread baked in 79 AD by “Celer, slave of Quintus Grainus Verus” found in an over in Pompeii and a fresco from the house of the baker depicting the daily buying of bread Applied Microbiology: Application of microbial concepts to address problems or create new processes or materials Preventing loss of food, crops, etc Food is food for more than you ∙ Properly harvested wheat is dry. Proper storage must also be dry o Improper grain storage mold called ergot (deadly) o Moisture Microorganisms o Grain is a staple ∙ Fruits and vegetables o Commercial wetsourcestorage irradiator o Blue glow: sonic boom in radio electric spectrum (Cherenkov radiation) ∙ Meats and eggs o Page 846 o Danger in gamma: can screw up DNA o FDA inspection (applied microbiologist) measuring temperature and microbiological o Sick toxin intoxications ∙ Fish and Shellfish ∙ Dairy o Tuberculosis can be found from milk o Microbes live in the utter ∙ Others o Coffee plant shows sign of leaf rust disease Caused by Hemileia vastatrix (microbe) Crop Loss ∙ Usually due to microbes Our Loss is Their Gain ∙ Surface microbes can cause rot ∙ Cantaloupes: salmonella o Surface Salmonella and Listeria species can sicken people ∙ Pasteurization of the surface of netted melons (cantaloupes) ∙ Gut, hide, or hoof flora can contaminate meats o USDA inspectors are microbiologists Look for diseases before and after slaughter Parasites may not be evident o Muscle tissue with Trichinella cysts (in pork) Worms in muscle o Hard shells are no guarantee Porous microbes can get in Seafood covered in microorganism ∙ Salmonella or Fibrio ∙ Dairy mechanization has greatly cut microbial contamination Modern Applications Foods Past and present ∙ Direct consumption o Spirulina; a cyanobacterium. Two edible species; Arthrospira platensis or Arthrospira maxima o Has all amino acids you need “super food” o Roasted nori sheets. Made from algal species the genus Porphyra ∙ Modification/ Preservation o Witbier, wine, cheese, bread, vinegar, meat (fermentation) ∙ Biofuels the potential future o Microbes have oil o Corn to ethanol (not good) o Algae (more efficient) if you can get process to work Modern Applications ∙ Simple organic compounds o Used directly or in other industrial synthesis ∙ Enzymes∙ Amino Acids o Animals use 20 o 8 must be ingested o Several can be made via microbial metabolism ∙ Antibiotics All are sourced from microbes ∙ Vaccines Used to come from animals ∙ Hormones Takeaways • Humans have been doing applied microbiology for at least as long as we have history for. • Microbes and applied microbiologists do a lot for modern humans. • Applied microbiology isn’t only about combating microbial spoilage. • The range of products produced by microbes varies widely from simple organic compounds, to complete foods, to human hormones. • Microbes can function in directly productive or modifying roles. • Careful tracking of species and strains is critically important in applied microbiology. Lecture 4 – Environmental Microbiology 1/18/17 Microbiology in the News ∙ Bacteria resistant to every antibiotic approved in the US ∙ August 18, 2016 – Woman in her 70s admitted to an acute care hospital in Reno, NV o Extended stay in India, hospitalized after fracturing her right femur o Seroma liquid between skin and incision; common after (on right hip) ∙ Collected sample on August 19th ∙ Bacterium from wound initially IDed as carbapenemresistant Enterobacteriaceae (CRE) o Carbapenems are “last resort” antibiotics ∙ Placed in single room with contact precautions ∙ Early September – Woman dies of septic shock ∙ CDC determined that the sepsis was caused by a Klebsiella pneumoniae strain that is resistant to 26 antibiotics, including all those available for treating humans o Expressing New Delhi metallobetalactamase (NDM) Common: India, China, Pakistan, Venezuela ∙ Reno has been watched for multidrugresistant bacilli since 2010 but this is the first NDM CRE found o No evidence yet that NDM escaped containment What is an environment? The air, water, minerals, organisms, and all other external factors surrounding and affecting a given organism at any time ∙ Ecology how organisms interact with one another and with their environment o Microbes play huge role in humans and other organism o Life needs bacteria ∙ Energy Flow Heat Heat Heat SUN Energy Producer** Consumer Decomposer Inorganic nutrient pool **Microbes make up most oxygen oceans (producers) Yeasts = Consumer ∙ Cycles o Water o Carbon (Figure 25.3) o Nitrogen (25.4) o Sulfur (25.7) o Phosphorus Air ∙ All major microbes types can be found ∙ Microbes don’t grow in air ∙ Cells and spores can be carried o Snow, rain, dust carries microbes ∙ Different environments = different organism ∙ Indoors? Lots of people? = Lots of microbes in the air o Especially fungi o Typical results of leaving a nutrient agar plate exposed to the air of a room Soil ∙ All the major microbes types are found here; bacteria are the most numerous ∙ Huge concentrations and diversity o 30,000 kinds in a single sample o Figure 25:11 ∙ Many of our antibiotics have been discovered in soil ∙ Soil microbes like Rhizobium species determine crop yields Water ∙ Every nutrient cycle that may happen on land also happens here o Earths surface is ~71% covered in water ∙ Virtually every aquatic organism is made of microbial carbon and they run on microbial energy Lecture 4 – Supplemental Material ∙ There are entire ecosystems that don’t require the sun but they still require microbes Sewage Treatment ∙ Will happen o Where do you want it to happen? ∙ Microbes – especially bacteria make it happen o Bacteria that come from your own colon Bioremediation ∙ Microbes can eat ALMOST anything – including crude oil o Aircraft spraying microorganisms directly onto oil spill surface o Crude oil spilled onto a beach Bioremediation workers in Alaska spraying nutrient solution to encourage microbe growth on oil contaminated surface and soils Lecture 5 Fundamentals of Chemistry 1/20/17 Matter & Energy ∙ Chemistry study of the composition, properties, and transformation of matter o Flow of energy from one place to another o Often fueled by the questions like, “What is this made of?” or “Where does this come from?” ∙ Microbiology implies chemistry since microbes are composed of and transform matter ∙ Chemistry has a long history; for much it, it didn’t look like chemistry ∙ Like other sciences, what we now call chemistry has gone through many stages o The Temple to Hathor, in Dendera Temple Complex Best Guesses ∙ One of the earliest precursors to chemistry for which we have a record is the ancient Egyption mythology of the Ogdoad, or the Eightfold (~2700 B.C) ∙ In the Eightfold, the primordial chaos is represented in four male/female pairings o The interplay between The Eightfold gave rise to Ra, sun god∙ These are evidence of attempts to describe the origin and properties of matter and energy o Males = frogs o Females = snakes Almost Alchemical ∙ Many of the stages, like The Eightfold, are, to modern people, indistinguishable from religion or philosophy ∙ Same could be said for Empedocles (490430 B.C.) that argued four elements (air, earth, water and fire) and two forces (love and hate) ∙ Truth that the sciences are always tied up with metaphysics, whether acknowledged by the practioners or not Small beginnings ∙ We currently understand it to be the Greeks Leucippus (400300 B.C.) and the Democritus (460370 B.C.) who proposed the idea of the atom ∙ The idea was highly disliked by Plato (427347 B.C.) who favored a four elements formulation ∙ Aristotle (384 322 B.C.) picked the subject up after his mentor died and added his own twist: Substance as a combination of matter and form o FIVE ELEMENTS: Fire Water Earth Air Ether ∙ It was formulations of the Aristotelian views that were popular for more than 1000 years There is Nothing New Under the Sun John Dalton ∙ Poor family background, taught kids at age 15 ∙ Dalton’s law ∙ Partial pressure AntonLaurent de Lavoisier ∙ Put down the fifth element theory How We Now Think ∙ Matter is composed of atoms, which are, in chemistry, treated like particles ∙ Atoms come in different flavors which we call elements ∙ Atoms of different elements differ from one another, mainly, by their number of protons o Neutrons and electrons aren’t irrelevant o Figure 2.1 ∙ Differing number of neutrons yield isotopes ∙ We (nonphysicists) generally care about atomic mass, charge, and location Bits and Bobs ∙ Elements are organized but atomic number which is the number of protons in its nucleus ∙ Protons and neutrons give elements its mass o Protons (+) o Neutrons ( ) o Electrons () May have different energy levels, in multiple shells ∙ Atoms with a full eight electrons in their outer shell are stable and don’t easily bond with others The Ions ∙ Atoms that have a nearly full or nearly empty outer shell have tend to forms ions o May be positive cation or negative anion ∙ Ions of either type are prone to lose or gain or share electrons until their shell (orbital) is filled Bonds of Affection ∙ Atoms can attach (bond) together in groups of two or more to form molecules o From New Latin moles “mass” ∙ Bonds between atoms of different elements are compounds ∙ O2 = molecule ∙ CO2 = compound ∙ All living things we know of are mostly made of compounds containing C,O and H o Others such as P, S, and N ∙ Main types of bonds o Ionic Opposites attract; formed by ions of different charges o Covalent Share electrons between atoms, common is carbon molecules, more stable o Hydrogen Molecules have differently charged regions, causing inter molecular ionic linkages, weaker than ionic but every important in living things Polar v Non Polar ∙ Like dissolves like ∙ A polar compound is one with different charge regions ∙ Water is polar ∙ Oil is nonpolar Water ∙ Polar; hydrogen bonds ∙ Good at dissolving ions ∙ Surface tension A byproduct of hydrogen bonding. High affinity for one another and not for gasses ∙ Specific heat – Water has high, can take in or release a lot of energy without changing temperatures ∙ Hydrolysis & dehydration synthesis – Water takes part in it, split bond with water and make something and water is byproduct Reactions Catabolism the breakdown of substances to release energy XY X + Y + energy = exergonic Anabolism The use of energy to make substances X + Y + energy XY = endergonic Acid, Bases and pH ∙ Cells are suited to certain ranges of environmental conditions o p = log o H= concentration of H+ = [H] o pH = log([H+]) ∙ Acid = donates H+ or accept OH ∙ Base = accept H+ or donate OH Organic Molecules ∙ Contain one or more carbon atoms covalently bound with hydrogen o May also contain other things o Even functional groups ∙ Carbohydrates o Main sources of energy. Can also be structural. May have isomers. Mono, Di, Polysaccharides. o ∙ Lipids (nonpolar – fats, steroids, phospholipids) o More energy than carbohydrates, harder to break their bonds o 2.14 o Fats, steroids, phospholipids. Dissolve well in nonpolar solvents. Can be used for energy (have more too). I important in cell membranes. ∙ Proteins o Made of amino acids; there are 20 . At least one NH2 and one COOH, differentiated by their Rgroup. Linked by peptide bonds. Primary, sec, tert. Disulfide linkages. Denaturation. ∙ Enzymes o A subset of the proteins that allow rxns to occur at life temperatures. They hold molecules close together in proper orientation. Active site & substrate. Hexokinase, ATP, Xylose, Mg2+ cofactor, adds PO4 to 6C sugars. ∙ Nucleic Acids o Polymers of Neucleotides = nitrogen base, 5carbon sugar, and some PO4. They can store energy, release it on command, and store information. DNA in helices with hydrogen bonds & RNA in single strands. Microscopy & Staining 1/23/17 A Relatively New Thing ∙ An outgrowth of optics o Greek optike “appearance or look” o Properties and phenomena of light visible/invisible and of vision o History may go back to 700 B.C. Nimrud of Layard Lens ∙ Originally there were at least two school of thoughts o Intromission Normally recognize how we see things (to let in) o Emission eyes sent out rays that perceived those things and sensory information back to us (to give out) Plato loved this theory Roger Bacon (12191292) ∙ Opus Majus contained De Scientia Perspectivae (Optics)∙ We have manuscript evidence of corrective lenses being in use from 1289 A.D. (according to Bologna Astronomical Observatory) o “…Glass lenses for spectacles recently invented, of great advantage to old people with weak vision.” ∙ We have pictorial evidence of the existence of wearable eyeglasses from before 1352 A.D. ∙ A series of advances, especially in lens manufacture, in the late 1500’s and early mid 1600’s gave rise to: o A Galileostyle telescope; Spy glasses (military inventions) o Microscopes; Thomas Hookestyle compound microscope Microscopy Principles ∙ Microscopy, Greek mikro and skopon “object, target, a mark (on which to fix your eye)” ∙ Basic principles o Convergent lenses o Divergent lenses o Special coating ∙ Units = metric o Ûm = micrometer= 106 m o Nm = nanometer= 109 m Nanometer micrometer meter Size Does Matter ∙ Wavelength Resolution ∙ Resolution objects that are separate look separate o Can you even see them? o Figure 3.4 ∙ Light & Objects o Figure 3.6 o Larger wavelength wore resolution you can see larger things o Refraction – Bending of light as it passes through media of different density (Figure 3.7, 3.9) o Diffraction – Bending of light as it passes through small openings (Figure 3.10) Microscopy Practical ∙ Light microscope o Physical light (see with eye) o Monocular or Binocular 1. Darkfield Microscopy (light shined through side) Good for living things 2. Phase Contract Microscopy Special condenser and objectives Designed to take advantage of refraction of light, as light passes through it is refracted differently 3. Nomarski Microscopy Specialized condensers, prisms, special way to orientate sample 4. Fluorescence Microscopy (VERY IMPORTANT IN MICROBIOLOGY) Use properties to visualize cells and use special dyes Stain mix culture, using green and red and can see membrane transport Samples with bacterial cells glowing Use to see very small cells, not 100% clean 5. Confocal Microscopy Fluorescent dyes, illuminating things with lasers Sharp images, captures layers 6. Electron Microscopy Magnetic lens Subcellular structure, acellular (ex. viruses) TEM – Transmission electron microscopy o Sends electron through things SEM – Scanning Electron microscopy o Dealing with metals (gold, platinum) STM AFM Specimen Preparation Wet mounts Smears Staining o Simple (one ingredient) Provides color to an organism Basic dyes = positively charged o Differential (Figure 3.3) takes more than one time to stain Allows viewing of any differences between organism Gram Ziehl Neelson AcidFast Negative Flagellar Endospore Not a magic bullet for identification Characteristics of Prokaryotic & Eukaryotic Cells 1/25/17 Where we Begin ∙ All living things we know of are cellular ∙ All cells can be classified as prokaryotic and eukaryotic o Greek pro “before”, eu“true” and karyon “nucleus” ∙ Prokaryotic o Before nuclei o Single celled Eubacteria (True) Archaeobacteria (Ancient) ∙ Eukaryotic o True nucleus o Many multicellular Plants Animals Fungi But NOT all of them ∙ Protists Prokaryotes Size: 0.52.0 um Divide by binary fission Shape: vary (Figure 4.1) o Coccus spherical o Coccobacillus ovalish o Vibrio comma shaped o Bacillus rodlike o Spirillum rigid,wavy shaped o Spirochete corkscrew Arrangements o Diploccous o EtcCell Wall o Gives cell shape, provides protection o Inhibit penicillin o Porous – allows things to pass through o Pressure resistant o Allatis – different layers o Very flexible, strong o Grand positive cells – up to 40 layers Bacteria cell walls made by polymer of peptidoglycan Grand Positive o Cell wall is very thick; only one layer – membrane directly under o Grand Negative o Cell wall is made up of pepitomic glycen; thinner o Outer membrane o Peryplasmic space active cells (metabolism, etc) Acid Fast o Outer membrane is made up fatty substance o Similar to grand negative Gram Staining Cell (plasma) Membrane o Heads polar o Tails nonpolar o Flexible o Fluid mosaic model (how membrane behaves) o Watch animations Internals o Cytoplasm o About 20% dissolved material, 80% water o Ribosomes o Sizes important o Nuclear Region “nucleoid” o Find DNA o Special Regions o Chromotaphores and nitrifiers o Inclusions o Solid, granulas o Endosporeso Cell within a cell o Tough, little water (crystalize when freezes so resistant to cold) o External o Flagella Tiny machine; different to adapt Rotate (spin) Axial filament (only in spirakytes) Pili ∙ Hair like projections ∙ When bacteria want to attach ∙ Conjugation (share chromosome material) Glycocalyx ∙ Slime coat/capsule Eukaryotes ∙ Membrane o Lipids and cholesterol imbedded into membrane o Much larger cells than prokaryotic o Different structures, +more o Divide by mitosis ∙ Internals o Cytoplasm o Nucleus o Mitochondrion Membrane bound organelle Energy production Own DNA Reproduce itself Get from mother; woman contribute one whole cell Males contribute only part of the cell, lose apart o Chloroplast Not all have, many do (plant like) Similar to mitochondria Two membranes (stacks of thylakoids) Photosynthesis occurs ∙ Uses light energy to synthesize carbohydrates o Ribosomes Imbedded on endoplasmic reticulum; extension of nuclear envelope Rough ribosomes Smooth Ribosomes are 60% RNA/ 40% protein o Golgi Apparatus Packages proteins, delivery Receive from ER, modify and ship out o Lysosome Digest, pathogens o Peroxisome Oxidant Contain peroxide, strong oxidizer Key destroyer of pathogens o Vacuoles Storage for fat, water, etc o Cytoskeleton Structural underpinning gives shape ∙ Externals o Flagella Swim around, sperm have flagella DO NOT SPIN; thicker, undulate o Cilia Projections, whip motion Shorter than flagella, more abundant, In humans respiratory tract o Pseudopodia False feet Figure 4.24 WBC o Cell Walls Some do, some don’t Algae – pellicles Endosymbiosis ∙ LOOK UP IN BOOK ∙ symbiosis in which one of the symbiotic organisms lives inside the other. Import/Export 1/27/17 ∙ Simple Diffusion o Function of temperature, density, abiotic factors o High conc Low concentration Works in liquids, solids ∙ Facilitated Diffusion o Create hole in membrane and line with proteins that only let certain things through Ex. Protein ions, glucose molecule ∙ Osmosis o Movement of water o From high conc. to low through membrane (semipermeable) Tonicity (osmosis) what is diffused into the water, salty ∙ Active transport o Move things against conc. Gradient Move from low to high conc. ∙ Endo/Exocytosis o Endocytosis invagination of membrane, create pocket Good to bring in specialized nutrients o Exocytosis vesicles export what’s in it, dump outside cell (requires energy) Good for immune system, extends pseudopods and take in bacterium and merge with lysosome to break it up, also works for viruses Essential Concepts of Metabolism Metabolism sum of all chemical processes carried out by living things; breakdown of things to get energy ∙ Figure 5.1 ∙ E donor/receptors Anabolism making of things, using energy; Reduction (gain electrons) Catabolism Oxidation (lose electrons) Auto/heterotrophy Heterotrophic Eats something besides it self (ex. Human) Autotrophic Organism itself is creating its own food (ex. Autoimmune disease, plants, photosynthetic algae) Photo/chemo ∙ Photoautotroph Making food using light ∙ Chemoautotroph Chemicals reactions to make carbon ex. Hot spring, deep sea vents ∙ Photoheterotrophs Get energy from sun but use outside sources as well ∙ Chemo heterotrophs Humans, get energy from chemical reactions and organic carbons o Pathogens ~ chemoheterotrophs Food = other cells (humans cells) Substrate Product Substrate Intermediates = everything Enzymes (better than heat) ∙ Activation energy (lowers) ∙ Endoenzymes o Works inside the cell ∙ Exoenzymes o Works outside the cell ∙ Active Sites ∙ Coenzymes/Cofactors Figure 5.7 ∙ Substrates anything enzyme acts upon ∙ Inhibition If you need to deactivate enzyme o Competitive inhibition = acts as “fake” substrate o Allosteric inhibition = changes the shape where the active site binds Not reversible, used in metabolic regulation Change rate ∙ Raise temperature o If you raise it too high, denature enzymes o Increase reaction rate Reaction Controls ∙ Temperature ∙ pH ∙ Concentration (AB – A.B) Anaerobic Metabolism ∙ Glycolysis o Nearly universal Can occur in presence of oxygen Virtually everything does it Converts glucose to pyruvic acid Occurs in the cytoplasm o Indifferent to oxygen o Four main bits Figure Book lists page 124 !!!! LOOK UP In: 1 glucose Out: 2 Pyr + 2 NADH + 2 ATP (net) Glycolysis IN 2 ATP OUT 4 ATP 2 NADH Fermentation ∙ A use for pyruvate ∙ Oxidizes NADH to keep glycolysis party going ∙ Some delicious and some are deadly Aerobic Metabolism – Respiration∙ Glycolysis as a prelude to more efficient processing of pyruvate ∙ Krebs Cycle – Double Trouble ALSO CALLED TCA ∙ Sir Hands Adolf Krebs (1930’s or 1940’s) o Tricarboxylic acid (TCA) cylcle o Citric Acid cycle Krebs: IN: OUT: 6 NADH, 2 FADH2 Krebs II 2 GTP 2 ATP 3 Main Points: ∙ Figure 1. Start Pyruvic acid from Glycolysis 2. Oxidation of carbon 3. 3 NAD made from NAD 4. GDP to GTP (same as ATP) ∙ Electron Transport & Oxidative Phosphorylation Chemiosmosis ∙ Pumping out hydrogens and using energy as they flow back in o Hydrogen ions causes pH goes down o Concentration goes up MORE HYDROGEN IONS = MORE ACIDIC o Falling down in energy as you go o Harvesting energy o Substrate comes in and generating and using coenzymes More = NADH Less = FADH2 ∙ Anaerobic respiration o Does not require O2 o Figure 5.21 o Uses other inorganic o NO3, So4, CO2
4 ATP & 2 NADH
6 NADH & 2 FADH2
2 GTP 2 ATP
o Often fueled by the questions like, “What is this made of?
o Where do you want it to happen?
What is an environment?
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Total: 10 NADH & 2 FADH2 = 30 ATP + 4 ATP = 34 ATP + 6 ATP = 40 ATP – 2 ATP = 38 ATP 1 NADH = 3 ATP 1 FADH = 2 ATP Essential Concepts of Metabolism 2/3 2/01/17 Metabolism applies to the sum of all chemical processes in living organisms The notion that disease could be prevented by proper disposal of human waste was developed? A In EARLY biblical times What are Robert Koch’s Postulates used for? C. Linking specific organism to a specific disease Which of these best illustrates a catabolic reaction? D. The formation of glucose molecules from a starch Phorphorylation ∙ The adding of a PO43 to something ∙ Transfers energy from one place to another Essentials Concepts of Metabolism The prokaryotic aerobic metabolism of glucose produces a total (net) of _____ molescules of ATP? A 83 B30 C34 36 DNone of these How is ATP formed by chemiosmosis? A) A charge difference of outer and inner membrane gives motive force to generate ATP B) Nitrate is used as their final electron acceptor C) The last step involves H2O to be splits into O2 D) All of the metabolites enter the Krebs cycle E) None of these What is the function of mitochondria? (OXIDATION) A) Store the cell’s primary genetic information B) Site of protein synthesis C) Carry out reductive reactions that provide power for the cell D) Help maintain the structure of the cell during division E) None of these is a function of mitochondria Metabolism of fats ∙ Catabolism o Breakdown of things ∙ Hydrolysis o Add water to split bonds ∙ CoA attachments how you get into the Kreb cycle to get NADH o Link to fatty acid chain ∙ Beta Oxidation o Enzyme comes in and breaks the bonds at some distant o Beta = two ∙ AcetylCoA right into Krebs ∙ What about proteins? o Atkins diet – eat only protein o Split into aminos o Deaminatedo Glycolized Ways cell can get energy – but not all cells can process for energy Other Metabolism 1) Photoautotrophy Using sun energy to generate carbon and ATP ∙ Two types: both include light and chlorophyll o Sometimes electrons come back to chlorophyll sometimes they do not HAPPENS ON MEMBRANES IN CHLOROPLAST ∙ Chloroplast has its own DNA o Noncyclic photoreduction o Cyclic Phosphorylation More common, eukaryotic plants or algae Chlorophyll and light 2) Photoheterotrophy o Need light and organic carbon ex.sugars 3) Chemoautotrophy o Hypothermal vents o Table 5.5 o Sources of energy are chemical in nature NH3 HNO2 FE2+ 4) Chemoheterotrophy o Get energy from environment from chemicals o Get organic carbon from organisms o HUMANS, FLESH EATING BACTERIA What to do with all that energy? Biosynthesis ∙ Amphibolic pathways o Intermediate products that can be used for energy or synthesiso Anabolic pathways o Making amino acids, 1012 steps before you get amino, all steps have enzymes and regulated ∙ Others are complex ∙ Lipids, carbohydrates, peptidoglycan, lipopolysaccharide (found in outer membrane) , etc. TCA = KREB CYCLE Other energy uses: ∙ Membrane transport o Moving things against concentration gradient Ex. Glucose o Moving big molecules Take them apart o Porins and Permeases Porins seen gram negative bacteria, transmembrane Permeases special set of proteins for facilitated diffusion ∙ Endo/exocytosis ∙ Taxis o Flagella o Cillia ∙ Bioluminescence o Microbes use energy to light up EXAM PRACTICE What good is fermentation? ∙ Takes hydrogen off of the NADH to do more glycolysis A way enzymes can be inhibited? 1) Allosterically inhibition ∙ Binds on enzymes and changes shape ∙ Usually permanent 2) Competitive inhibition o Another molecule binds to active site o Usually reversible o Non substrate molecule binds to active site so occupies enzyme What is abiogenesis?Idea that living things spontaneously from non living material What is the significance of resolution and microscopy ? Wavelength of light (radiation) the smaller wavelength the better resolution Shorter wavelength the worse resolution Different types of microscopes? Difference between gram negative and gram positive? Main difference = thickness of peptodine cell wall Gram negative – have secondary membrane with space Gram positive – simpler Function of a bacterial cell membrane? Regulate the movement of materials into and out of the cell Which of the following means chains of sphere shaped bacteria? Streptococcus Movement away or toward light Phototaxis Which of the following can bind to an enzyme’s active site? Competitive inhibitors and substrates Surface of a virus – Use Scanning Electron Microscopy Email: Who proved biogenesis wrong in the mid – 1800s? Will you be using pictures in your exam similar to the homework or from the textbook Question 59 on the homework, I got the answer but was hoping youd be able to refer me to where I can read more on that and figure it out if it was another question similar to this on the exam?