STUDY GUIDE FOR THE MICR 3100 FINAL EXAM-Spring/20. Study Materials and content from Chapter 1-24. Best for quick exam preparation.

STUDY GUIDE FOR THE MICR 3100 FINAL EXAM-Spring/20 Date & time: MICR 3100-6 Monday, May 14, 9:30-11:30 AM at SH C136 MICR 3100-1 Tuesday, May 15, 12:00 AM to 2:00 PM at FA 219 ...

STUDY GUIDE FOR THE MICR 3100 FINAL EXAM-Spring/20 Date & time: MICR 3100-6 Monday, May 14, 9:30-11:30 AM at SH C136 MICR 3100-1 Tuesday, May 15, 12:00 AM to 2:00 PM at FA 219 Total points: 200 Multiple choices/true and false/matching, short answers and fill ins, short comprehensive assays. Ch.1: - How those great scientists contributed to developing the science of Microbiology and related fields (match): - Robert Hooke:  Built the first compound microscope  Used it to observe mold  Published a manuscript that showed objects under the microscope  Coined the term “cell” Antonie van Leeuwenhoek:  Built the single-lens magnifiers, complete with sample holder and focus adjustment  First to observe single-celled microbes  Called them “small animals” Louis Pasteur:  Disproved the spontaneous generation theory  Created “swan-neck” flasks- the contents remain free of microbial growth, despite access to air  Discovered the microbial basis of fermentation  Developed the first vaccines based on attenuated (weakened) strains: Fowl Cholera and rabies  Immunization Robert Koch:  Founder of the scientific method of microbiology  Applied his methods to numerous lethal diseases around the world  Chain of Infection or transmission of a diseases: an important principle of epidemiology  Growth of microbes in Pure Culture  Koch’s Postulates Alexander Fleming:  Discovered Penicillium- generated to substance that kills bacteria Lynn Margulis:  Modified the five kingdoms dramatically  Endosymbiosis theory: the eukaryotic organelles are evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes • Mitochondria: proteobacteria • Chloroplasts: cyanobacteria Carl Woese:  Discovered and found prokaryotes that lived in hot springs and produced methane have DNA genomes very different from all other known life forms.  He called them Archaea  Discovered Archaea  Discovery replaced the scheme of five kingdom with three equally distinct groups: Bacteria, Archaea and Eukarya .  Archaea living in extreme environments produce exceptionally sturdy enzymes that can be used for industrial processes and for clinical identification procedures such as PCR amplification of DNA - Understand Koch’s postulates • Criteria for establishing a causative link between and infectious agent and diseases 1. Microbe is always present in diseased host - Absent in healthy 2. Microbe is grown in pure culture - No other microbes present 3. Pure microbe is introduced into healthy host - Individual becomes sick 4. Same microbe is re- isolated from now sick individual Ch.2: Excluded Ch.3: - The cell-membrane lipid diversity in different bacteria, different environmental conditions and between bacterial and other domains (archaea and eukarya). Cell Membrane Lipid structure • Membranes have equal parts of phospholipids and proteins Membrane Lipids • Phospholipid- has glycerol with ester links to two fatty acid and a phosphoryl head group • Leaflets- two layers of phospholipids Membrane Proteins • Structural support  Some membranes proteins anchor together different layers of the cell envelope  Other proteins attach the membrane to the cytoskeleton or form the base structure extending out from the cell such as flagella • Detection of environmental signals • Secretion of virulence factors and communication signals  Membrane proteins complexes export toxins and cell signals across the envelope • Ion transport and energy storage  Transport proteins manage ion flux between the cell and the exterior, ion transport generates gradients that store energy Transport across the Cell Membrane • The cell membrane acts as a semipermeable barrier • Selective transport is essential for survival • Passive Diffusion- small uncharged molecules like O2, CO2 and water can easily permeate the membrane  Some molecules like ethanol can disrupt the membrane—which can make molecules toxic to cells  Large strongly polar molecules (sugars) and charged molecules (amino acid) cannot penetrate the hydrophobic interior of the membrane and requires transport by specific proteins  Water molecules permeate the membrane, but rate of passage is increased by protein channels called aquaporin • Osmosis-Water tends to diffuse across the membrane into the cell causing the expansion of cell volume • Membrane-permeant weak acids and weak base- exist partly in an uncharged form that can diffuse across the membrane and increase or decrease, respectively, the H+ concentration within the cell • Transmembrane ion gradients- polar molecules and charged molecules require transport through specific protein transporters  Passive transport: molecules move along their concentration gradient  Active transport: molecules move against their concentration gradient Membrane Lipid Diversity • Environmental stress:  Starvation stress increases bacterial production of lipids with an unusual type of phosphoryl head group  Cardiolipin or diphosphatidylycerol: a double phospholipid linked by a glycerol - Concentration increase in bacteria grown to starvation - Localizes to the cell poles + Binds certain environmental stress proteins  The fatty acid of phospholipids also very - Fatty acid chains may be unsaturated - May also contain cyclic structures  Membranes also include planar molecules that fill gaps between hydrocarbon chains - In Eukaryotic membranes: sterols like cholesterol - In bacteria: Hopanoids or hopanes- fit between the fatty acid side chains of membranes and limit their motion, thus stiffing the membrane.  Archaea have unique membrane lipid - Archaea have the most extreme variations in phospholipid side- chain structures - All archaeal phospholipids replace the ester link with an ether link(C-O-C) - Archaeal hydrocarbon chains are branched terpeniod - Terpeniod- polymeric structures derived from isoprene, in which every fourth carbon extends a methyl branch - The structural differences in the cell wall of gram-positive, gram-negative bacteria and mycobacteria and between bacteria and archaeal and eukaryotic microorganisms. • Peptidoglycan Structure  Most bacterial cells are made up of peptidoglycan  Long chains of peptidoglycan consist of: o N-acetylglucosamine o N-acetylmuramie  Peptidoglycan is unique to bacteria  The enzymes responsible for its biosynthesis make excellent targets for antibiotic • Cell Wall of gram-positive bacteria (Firmicutes)  Have thick cell wall  3-20 layers of peptidoglycan threaded by teichoic acid  The capsule- made of polysaccharide and glycoprotein o Protects cells from phagocytosis o Found also in gram-negative cells  S-layer o An additional protective layer found in free-living bacteria and archaea o Crystalline layer or thick subunits consisting of protein or glycoprotein o May contribute to cell shape and help protect the cell from osmotic stress • Cell wall of gram-negative bacteria (Proteobacteria)  Have a thin cell wall  1-2 layers of peptidoglycan enclosed by an outer membrane  Covered by an outer membrane, which confers defensive abilities and toxigenic properties on many pathogens  Inward-facing leaflet includes lipoprotein  Outward-facing leaflet contains: o Lipopolysaccharides o Porins • Mycobacteria  Have a complex multilayered enveloped (cell wall)  Includes defensive structure such as mycolic acids  Include unusual membrane lipids (mycolic acids) and unusual sugars (arabinogalactans) Ch.4: - Bacterial role in the nitrogen cycle (read from the book) Nitrogen fixation: possess nitrogenase, which converts N2 to ammonium ions (NH4+) o Nitrogen fixing bacteria may be free-living in soil or water or they may form symbiotic associations with plants or other organism Nitrification- group of bacteria gains energy by converting or oxidizing ammonia to form nitrate o Form of lithotrophy Denitrification- other heterotrophic microbes can reduce nitrate to N2 o A process that uses nitrate and related inorganic forms of nitrogen as terminal electron acceptors for certain electron transport chains o Denitrifying bacteria send an amount of nitrogen into the atmosphere that roughly balances the amount removed by nitrogen fixation - Transport of materials across the cell membrane. Facilitated Diffusion: solutes move across a membrane from a region of high concentration to one of lower concentration o Ex: the aquaporin family that transports water and small polar molecules such as glycerol - Active Transport Requires Energy: o Coupled transport system: driving ion moving down its gradient is used to move a solute up its gradient o In symport, the two molecules travel in the same direction o In antiport, the actively transported molecule moves in the direction opposite to the driving ion - ABC Transporters are Powered by ATP: the largest family of energy-driven transport system is the ATP-binding cassette superfamily (ABC transporters) o Two main types: o Uptake ABC transporters are critical for transporting nutrients o Efflux ABC transporters are generally used as multidrug efflux pumps - Siderophores Scavenge Iron: o Siderophores are specialized molecules secreted to bind ferric ion (Fe3+) and transport it into the cell o The iron is released into the cytoplasm and reduced to the more useful ferrous (Fe2+) form ::::::::::::::::::::::::::::::::::::::::CONTENT CONTINUED IN THE ATTACHMENT:::::::::::::::::::::::::::::::::::::::::::::::::::