MICR 3050 Test 2 Study Guide
MICR 3050 Test 2 Study Guide MICR 3050 - 002
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This 12 page Study Guide was uploaded by Isaac Baum on Friday October 7, 2016. The Study Guide belongs to MICR 3050 - 002 at Clemson University taught by krista barrier rudolph in Fall 2016. Since its upload, it has received 53 views.
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Date Created: 10/07/16
Key Term– know definition Key Concept – understand description Study Guide for MICR 3050, TEST 2 (Fall 2016) Isaac Baum Chapter 3.6– 3.9 1. Describe the following bacterial structures and their functions: cytoskeletal proteins, cell inclusions, fimbriae, pili, flagella, and endospores. • Cytoskeletal proteins o FtsZ proteins Think: Z for “zipper” Purpose: line up in the middle of the cell to form the plane of division o MindD proteins Purpose: prevents polymerization of FtsZ at the poles of the cell to ensure even division o MreB proteins Propose: determine cell shape by forming the scaffolding for peptidoglycans to build the cell wall • Cell inclusions o Aggregates of organic or inorganic material o Cell inclusions are NOT organelles o Purpose: storage (bacteria store them up when there is excess, and deplete them when they need them later) o Types of inclusions: Carbon storage inclusions (store carbon in glycogen and PhB) Polyphosphate granules(store phosphate) Globules (store sulfur) • Note: these are stored in the periplasm Cyanophycin granules(store nitrogen) Gas vacuoles • Provide buoyancy • Permeable to gases but not water • Bacteria with these are found in water columns and can easily move up and down the water column. Magnetosomes • Detect north and south using Earth’s magnetic field • Bacteria with these are found at the bottom of water columns • Held in invaginations of the plasma membrane • Fimbriae o Short, hairlike appendages o Protein-based o Extremely numerous o Extend from the cell envelope o Purpose: attachment of the cell to surfaces (for some bacteria also motility of cell or DNA uptake) • Pili o Mostly the same as fimbriae o Sex pilus Special type of pilus that is longer and less numerous Used in conjugation Genes for sex pilus are found on plasmids • Flagella o Threadlike appendages, much longer than fimbriae or pili Key Term– know definition Key Concept – understand description o Bacteria flagella are rigid (eukaryotic flagella are flexible) o Purpose: motility, swarming, attachment, burrowing o Flagella have a lot of antigens on them, triggering the human immune response o Flagellar arrangements: Monotrichous – only one flagellum Polar – found at the end of the cell Polar monotrichous – one flagellum at the end of the cell Amphitrichous– two flagella, one at each end of the cell Lophotrichous– cluster of flagella at one or both ends Peritrichous – flagella spread out over the entire surface of the cell, pointing in all directions • Endospores o Dormant structures that are extremely resistant to bad conditions (more information is found in question #5 of this chapter) 2. Describe flagellar structureand movement. • Flagellar structure o Parts: filament, hook, basal body o Gram-negative Four rings L ring – embedded into the LPS layer P ring – embedded into the peptidoglycan layer MS ring – (Membrane Supra) within the outermost layer of the cytoplasmic membrane C ring – connected to the cytoplasm The MS and C rings can spin The L and P rings are stationary Fli proteins – control switches to turn the flagellum on and off o Gram-positive Two rings because there are fewer cell layers • Movement o Rotor produces torque, torque acts on stator (specifically on Mot A and Mot B proteins) o Proton motive force is used as the energy source (NOT ATP) Hydrogen ions accumulate just outside the plasma membrane • Result of electron transport chain Electric potential/potential energy generated across membrane Allowing the hydrogens back into the cytoplasm provides energy to spin the rotor 3. Define chemotaxis and describe how bacteria move toward an attractant (or away from a repellent). • Bacterial movement o Run Counterclockwise (CCW) rotation of flagella Always in one direction o Tumble Clockwise (CW) rotation of flagella A turning in place o Not all bacteria can tumble A bacterium that cannot tumble will sit and drift in the environment to change directions. o A peritrichous bacterium bundles its flagella together to move in one direction, and spreads its flagella apart to tumble. o Chemotaxis Key Term– know definition Key Concept – understand description Chemoattractants • Bacteria will run more and tumble less • Runs will last longer (called a “biased random walk”) • Goal: get to the attractant faster Chemorepellants • Bacteria will tumble more and run less • Runs will not last as long • Goal: change directions to head away from repellant 4. Describe other types of motility (spirochete, twitching, and gliding). • Spirochete (corkscrew-shaped bacteria) o Individual bacterium movement o Flagella are bound into an axial fibril Axial fibril winds around the cell Located in the periplasmic space o Spinning of axial fibril causes bacterium to flex and spin o Allows bacterium to better burrow into tissue • Twitching o Colony movement o Uses type IV pili and slime o Short jerky movements (bacteria use the pili to pull themselves along a surface) • Gliding o Colony movement o Smooth oozing movement o Only on solid surfaces o Exhibited by bacterial slimes 5. Understand the structure and functions of bacterial endospores, the basics of sporulation and germination, and endospore resistance. • Endospore structure o Exosporium – outside layer, made out of protein, thin and delicate o Spore coat – made of numerous proteins layered on top of each other o Protective outer membrane o Cortex – made of peptidoglycans o Core – contains the actual bacterium, dehydrated with no activity inside • Endospore function o Protect the bacterium in bad conditions • Endospore resistance o Calcium dipicolinate – not found in vegetative cells, protects DNA by surrounding individual bases o SASPs – proteins that protect DNA by binding to it, usedas a food source during germination o pH lowered – inactivates enzymes without denaturing them o extra outer coats (exosporium and spore coat) • Sporulation vs. germination o Sporulation Internal cell division (happens inside the cell wall) DNA becomes denser Septum grows around protoplast (which becomes the endospore) Original cell lyses to release the spore Can take 8 to 10 hours o Activation Key Term– know definition Key Concept – understand description Activated by gentle heating An activated spore is ready to germinate but not committedyet. o Germination Starts when good amounts of nutrients are detected Spore coat is ruptured Enzymes are reactivated Spores lose their high resistance as they germinate Spore will take in water and swell Chapters 11.1, 10.1 – 10.4 6. Know the requirements for microbial survival and growth and their sources. • Requirements for microbial survival o Energy source o Source of electrons o Nutrients All bacteria need C, H, and O Some bacteria may need other nutrients as well 7. Define and recognizethe major nutritionaltypes of microorganisms based on their energy source, electron source, and carbon source. • Classification based on energy source o Chemotrophs– energy source is chemical o Phototrophs – energy source is sunlight • Classification based on electron source o Chemoorganotrophs – energy source is organic chemicals To be organic, a chemical needs to have both C and H o Chemolithotrophs– energy source is inorganic chemicals • Classification based on carbon source o Heterotrophs – carbon comes from organic molecules Same organic molecules usually also serve as energy and electron sources o Autotrophs– carbon comes from carbon dioxide Energy and electrons come from other sources 8. Define metabolism, catabolism, and anabolism. • Metabolism – the total of all chemical reactions occurring in the cell • Catabolism – (think: cat tearing things apart) the part of metabolism that breaks down molecules and fuels reactions in anabolism. Generates energy and provides reducing power. • Anabolism – the part of metabolism that builds more complex organic molecules from simpler ones; requires energy and building blocks from catabolism. 9. Understand the concepts of free energy (G) and standard free energy change (∆ G ′). • Free energy (G) o Defined as the amount of energy that is available to do useful work • Change in free energy (ΔG) o The change in energy that can occur as a result of chemical reactions • Standard free energy change (∆G ′) o Defined as the standard free energy change at pH 7, temperature 25 deg C, pressure of 1 atm, and reactants and products at 1 M concentration. 10. Distinguish between exergonic and endergonic chemical reactions and theirrelationship to ∆ G ′. Key Term– know definition Key Concept – understand description • Exergonic reactions o Reaction proceeds spontaneously o o ∆G ′ is negative o Energy is released (ex = energy out) • Endergonic reactions o Reaction does not proceed spontaneously o ∆G ′ is positive o Energy is required (end = energy in) 11. Explain the importance of ATP. ATP is important because it stores energy to be used by other places and processes in the cell. It is the “energy currency” of the cell. 12. Be aware of other high-energycompounds, and know the change in standard free energy requirement for cells to use them. • Other high energy compounds exist (besides ATP) o The change in standard free energy needs to be negative for a cell to use them 13. Understand redox reactionsoincluding the standard reduction potential0(E ′) of half reactions, the electron tower, and their relationship to ∆G. • Half-reactions o Oxidation – removal of an electron o Reduction– gain of an electron o Protons commonly travel with the electrons • Equilibrium constant(E0′) o E0′ is a measure of the reducing agent to lose electrons o Electron donor – negative 0 ′ o Electron acceptor – positive0E ′ • Electron tower o The greater the difference between the 0 ′ of the donor and th0 E ′ of the acceptor, the more negative ∆Go′ is. o Electrons start at the top of the tower and move to various carriers down the tower. o The further the electrons fall down the tower, the more energy they will release. o Electrons always move from a reduced molecule to an oxidized molecule, and the oxidized molecule will then become reduced and the original molecule will be oxidized. o In a redox couple, the oxidized form of the molecule will be on the left and the reduced form is on the right. 14. Describe the location, organization, and functionsof the Electron Transport Chainsin bacteria. • ETC o Located in the plasma membrane (bacteria do NOT have mitochondria) o Function: to act like a small electron tower, transmitting electrons down the tower to generate energy o Organization: electron carriers arranged so that the first carrier has the most ne0ative E ′, and each successive electron carrier has a less negat0ve E o The ETC is responsible for generating the proton motive force 15. Define the two classes of electron carriers. • Coenzymes Key Term– know definition Key Concept – understand description o Freely diffusible, moveable o Transfer electrons from place to place o Example: NAD • Prosthetic groups o Firmly attached to plasma membrane, immovable o Example: cytochromes 16. Describe how NAD /NADHand NADP /NADPH carry electrons and their roles in metabolism. • NADH and NADPH are good electron donors • NADH and NADPH are reduced, while NAD +and NADP are oxidized + • NAD receives two electrons and one proton to become NADH • NADH transfers electrons from glycolysis and the Krebbs cycle to the ETC • NADH is used for catabolism, NADPH is used for anabolism Chapter 11.2 – 11.8 17. Compare and contrast aerobic respiration, anaerobic respiration, and fermentation in bacteria. • Aerobic respiration o Oxygen is final electron acceptor o Uses ETC and proton motive force o Makes ATP primarily by oxidative phosphorylation (also uses substrate-level phosphorylation) • Anaerobic respiration o Uses an exogenous acceptor (or sometimes an organic acceptor) other than oxygen o Uses ETC and proton motive force o Makes ATP primarily by oxidative phosphorylation (also uses substrate-level phosphorylation) • Fermentation o Uses an endogenous acceptor (e.g. pyruvate) rather than oxygen o Does not use an ETC or proton motive force o Makes ATP only by substrate-level phosphorylation 18. Compare and contrast substrate-level phosphorylation and oxidative phosphorylation. • Substrate-level phosphorylation – making ATP using direct transfer of a phosphate group to ATP • Oxidative phosphorylation– making ATP using proton motive force generated by the ETC 19. Describe aerobic catabolism (overview). • Aerobic catabolism o Catabolizes an energy source (e.g. glucose) to carbon dioxide o Uses glycolysis, TCA cycle, and ETC o Electron carriers are recycled o Maximum total yield of ATP: 32 4 ATP from substrate-level phosphorylation 28 ATP from oxidative-level phosphorylation • Uses NADH and FADH 2 20. Describe the organization and functions of the electron transport chain in aerobic respiration including its role in ATP production. • ETC in aerobic respiration o Series of electron carriers o Electrons flow from carriers with more negative E0’ to carriers with more positive E0’ o transfer electrons from NADH and FAD2 to a terminal electron acceptor Key Term– know definition Key Concept – understand description NADH produces 2.5 ATP FADH p2oduces 1.5 ATP o as electrons are transferred, energy is released to make ATP by oxidative phosphorylation 21. Understand the Chemiosmotic Hypothesis. The chemiosmotic hypothesisdescribes process of oxidative phosphorylation to make ATP. The ETC establishes the proton gradient (the proton motive force) across the plasma membrane by moving protons up the concentration gradient and out of the cell, where they will sit just outside the membrane. 22. Explain the function of ATP synthase. ATP synthaseacts as a gate that allows protons to flow back down the gradient and into the cell, and their energy is used by ATP synthase to synthesize ATP. 23. Know the functions of proton motive force and how it is established. The proton motive force is used for both ATP production and for spinning of flagella.It is established by the electron carriers of the ETC. The proton motive force stores energy in the form of a proton gradient across the plasma membrane. 24. For aerobic respiration, explain where in the pathway ATP is produced (glycolysis, TCA cycle, and ETC), the methods of ATP production used for each ATP generated, the electron carriers used, and the number of ATPs produced (during the process and the final net yield). • Glycolysis o Produces 2 ATP (substrate-level phosphorylation) o Produces 2 NADH • Acetylation o Produces 2 NADH • TCA cycle o Produces 6 NADH o Produces 2 FADH 2 o Produces 2 ATP(substrate-level phosphorylation) • ETC o Uses the 10 NADH and 2 FADH 2roduced by the other three o Produces 10*2.5 + 2*1.5 = 28 ATP (oxidative phosphorylation) • Total o All NADH and FADH 2s recycled o 4 ATP produced by substrate-level phosphorylation o 28 ATP produced by oxidative phosphorylation o 32 ATP produced total 25. Summarize the major features of the Entner-Doudoroff pathway. • An alternative glycolysis pathway • Used by some soil bacteria • Yields pyruvate and G3P • Key intermediate: KDPG • Net yield: 1 ATP, 1 NADH, 1 NADPH (when coupled with the second half of Embden-Meyerhof, which is normal glycolysis) 26. Describe the process of fermentation, its functions, and its products. • Fermentation o Takes place in the absence of an exogenous electron acceptor o Uses pyruvate or a derivative as the final electron acceptor Key Term– know definition Key Concept – understand description o Uses only substrate-level phosphorylation o Produces fermentation products to serve as electron dumps 27. Know why bacteria produce fermentation productsand how these products are useful to humans. • Bacteria o Use fermentation products to serve as electron dumps • Humans o Use fermentation products for food (e.g. bread, wine, cheese, yogurt, pickles) 28. Distinguish between homolactic and heterolactic acid fermentation. • Homolactic o Used to make cheese, sour cream, and yogurt • Heterolactic o Used to make sauerkraut, pickles, and buttermilk o Also causes food spoilage 29. Distinguish between mixed acid and butanediol fermentation. • Mixed acid fermentation o Uses several different fermentation pathways simultaneously o Tested by using the Methyl Red test • Butanediol fermentation o Uses only one fermentation pathway o Tested using the Voges-Proskauer test Detects acetoin, an intermediate product 30. Explain the purpose of the MR-VP test and know how it works. The MR-VP test uses both the Methyl Red and Voges-Proskauer tests to test for fermentation. If a bacteria tests positive for one of the two, it should test negative for the other. Chapter 7.1, 7.3– 7.4, 7.6 – 7.7 31. Describe the growth of bacterial cells (binary fission). • Binary fission o Cell elongation o Genome is replicated and separated o Cell division Septum forms at the middle of the cell o Increase in cell number 32. Describe in detail the four phases of bacterial growth observed in a batch culture. • Lag phase o Purpose: cell needs to replenish materials and reactivate enzymes, as well as adapt to new environment o Varies in length o Growth rate is increasing • Log (exponential phase) o Population will double every fixed time interval o Growth rate is constant and maximal o Bacteria are healthiest in this phase. • Stationary phase Key Term– know definition Key Concept – understand description o ph 7 is neutral o pH >7 is basicor alkaline o pH <7 is acidic o A bacterium can only live in a small range of pH values, usually no more than 2 or3 units o Most bacteria like pH 7 o Most bacteria maintain an internal pH of 7 even if they live in other pH environments Microbes can buffer their environment to control the outside pH Acid shock proteins • Keep proteins form denaturing under a sudden increase in acidity • Sudden increase needsto be small Waste products can maintain environment pH as well • Temperature o Bacteria cannot maintain internal temperature o Minimum point – lowesttemperature bacteria can survive o Maximum point– highest temperature bacteria can survive o Optimum point– best temperature, enzymatic reactions will occur at highest rate • Oxygen o Some bacteria need oxygen, while some can be killed by oxygen. Still others don’t need to use it but prefer to if it is available. 37. Be able to name, recognize, and define the types of microorganisms that grow in various environments, and know the adaptations they have made to live there. • Classification based on salt o Nonhalophile– does not require NaCl, only grows if < 1% NaCl o Halotolerant – do not require NaCl but can survive in some amounts o Halophile – require NaCl, grow best in 1-15% NaCl o Extremehalophile – require 15-30 % NaCl • Classification based on pH o Acidophiles– grow best in acidic pH(pH 0 – pH 5.5) o Neutrophiles – grow best around neutral pH(pH 5.5– pH 7) o Alkaliphiles – growbest in alkaline pH (pH 8.5 – pH 11.5) • Classification based ontemperature o Psychrophiles– prefer cold temperatures o Mesophiles– prefer warm temperatures (e.g. body temperature) o Thermophiles– prefer hot temperatures (think: hot springs) o Hyperthermophiles– prefer boiling temperatures (these are usually archaeons) o Psychotrophs– have a larger range that includes both cold and warm temperatures These can grow both in the refrigerator and in the human body • Classification based on oxygen o Aerobe– growsin the presence of oxygen o Obligate aerobe – requires oxygen to grow o Anaerobe– growsin the absenceof oxygen o Obligate anaerobe – is killed by the presence of oxygen o Microaerophile – requires a smallamount of oxygen but not too much (2-10%) o Facultative anaerobe/aerobe (the two are the same thing) – does not need oxygen but prefers it o Aerotolerant anaerobe – grows with or without oxygen 38. Explain how microorganisms protect themselves from the toxic products of oxygen reduction. • Reactive oxygen species o Toxicto bacteria o Examples: supraoxide radical, hydrogen peroxide, hydroxyl radical Key Term– know definition Key Concept – understand description o Anaerobes produce protective enzymes Examples: superoxide dismutase, catalase, peroxidase DISEASES Disease Cause Microbe Route of Characteristic Characteristics Transmission Symptoms Strep Throat S. pyogenes Gram positive, Respiratory Fever, sore throat, Round bacteria droplets from an red tonsils, linked together in infected person enlarged neck chains lymph nodes (sometimes also scarlet fever) Cholera V. cholerae Gram negative, Human feces Diarrhea (can also comma-shaped (usually bywater have vomiting or bacteria and food that has muscle cramps) been contaminated) Bacterial N. meningitidis Gram-negative, Saliva and Fatigue, fever, and Meningitis round bacteria that respiratory headache (can group in pairs secretions progress to neck (coughing, stiffness, coma, sneezing, kissing, and death) chewing on toys) Lyme Disease Borrelia type Spirochetes Infected ticks Expanding area of (Borrelia mayonii non-itchy redness, and Borrelia fever, headache, stricto in North tiredness America) Infectious Epstein–Barr virus Double helix DNA Primarily spread Fever, sore throat, Mononucleosis through saliva enlarged lymph nodes in neck, tiredness Gas Gangrene C. perfringens Gram-positive, rod- Primarily spread Muscle tissue shaped, anaerobic, through skin death, gas spore-forming breakage by a production, and foreign object like sepsis (damage to a military projectile body caused by the immune response)
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