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Exam 2 Week 3 Notes 2/19/16- 2/26/16

by: Luke Holden

Exam 2 Week 3 Notes 2/19/16- 2/26/16 3050

Marketplace > Clemson University > Microbiology > 3050 > Exam 2 Week 3 Notes 2 19 16 2 26 16
Luke Holden

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Here are Week 3 Notes for Exam 2! Covers 2/19/16 - 2/26/16. Great notes if you missed class or if you just want to want some explanations for some of the concepts. Like all of the other notes, they...
General Microbiology
Dr. Rudolph
Class Notes
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This 18 page Class Notes was uploaded by Luke Holden on Friday February 26, 2016. The Class Notes belongs to 3050 at Clemson University taught by Dr. Rudolph in Winter 2016. Since its upload, it has received 44 views. For similar materials see General Microbiology in Microbiology at Clemson University.


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Date Created: 02/26/16
Exam 2 Week 3 Notes 2/19/16 Energy and Work  Energy o Capacity to do work or cause change o G= Free energy (Gibbs Free Energy) o Δ G­ How much energy do we have now after we have already done the  reaction to completion  Can be positive or negative  Δ G= (­)= Spontaneous  Δ G= 0= Equilibrium  Δ G= (+)= non spontaneous  Work carried out by microorganisms o Chemical work­ synthesis of cellular material o Transport­ take up of nutrients, cell repair, and replace, elimination of  wastes, and ion balances o Mechanical­ motility of the cells­ chemotaxis  Standard Free Energy Change­ this the free energy change when: o pH 7 o 25  C o 1atm o 1 M o The symbol : G ´o Free Energy Change: KNOW THIS CHART LIKE CRAZY Metabolism Catabolism Anabolism Fueling Reactions Synthesis of complex organic molecules (glucose) from simpler ones (ATP) Energy conserving reaction Requires energy and building blocks from fueling reactions Provide reducing power electrons Generates precursors for biosynthesis ON  CONSTANT CYCLE BETWEEN THE TWO Energy Currency of the cell  ATP­ Adenosine Tri­phosphate o The phosphoanhydride bonds that attach the last two triphosphates to the bon are  high in potential energy because they are easy to make and easy to break o If you break 1 bond you will release ­31 kJ/mol o If you break 2 bonds you will release ­46 kJ/mol  Why the negative? Because this reaction is spontaneous and is releasing  energy  Why is it 46 for the next one and not 62? Because as you get closer to the  sugar, the bond becomes more difficult to break and thus causing a net  energy gain of ­46 kJ/mol.  o Role of ATP in Metabolism  The role is to make non spontaneous reactions spontaneous because the  cell has too.  o The big picture with ATP  Like the economy, money is cycled around and around to make the world  run.  In cells, the ATP is cycled around and around to make the cell run.  SO… to make money, (ADP ATP) you have to have an asset (Aerobic  Respiration, Anaerobic Respiration, Fermentation, Phototrophy, and  Chemolithotrophy)  SO… to get stuff you need (chick fila! Or more prevalent chemical or  transport work) you need to spend money (ATP)   However, the cell must be efficient with its time because it needs a certain  amount of ATP to survive and if it does not make it in time the cell will  die  CELLS ONLY USE REACTIONS THAT RELEASE GREATER  THAN  ­30 kJ/mols  Such as the ones give below o  Know this chart!!!!  Oxidation Reduction Reactions o Many metabolic processes involve electron transfers o Carriers are used to transfer electrons from electron donors (oxidizing agent) to  electron acceptor (reducing agent) + o Often results in things being restored (NAD  NADH) o OIL RIG  Oxidation involves loss   Reduction involves gain  Electron Donating Half Reaction o o Electron accepting half reaction o o Therefore: o o Half Reactions are always written as reduction reactions  H 2reaction is the best electron Donor  O 2is the best electron acceptor  Standard Reduction Potential (E’O) o Equilibrium constant for an oxidation reduction reaction o Measure of the reduction agent to lose electrons  More NEGATIVE E’O= better electron donor  More POSITIVE E’O = better electron acceptor o Electron tower  2 H/ H 2  ½ O 2 H 2  The greater the difference in E’O between the donor and the acceptor the  more negative Δ G= more spontaneous   When you receive an electron tower problem, always arrange it  from negative to positive (Negative at the top and Positive at the  bottom) Sample Question C4H4O4/C4H6O4  +0.31 V 2H / H 2 ­0.5 V Between these two reactions what reactant or product will be the electron donator?  (H2) Between these two reactions, what will be the electron acceptor? (C4H4O4) TO SOLVE THESE PROBLEMS WITH NO SWEAT: 1. Arrange the reactions with the most negative on top of the other 2. The top right product of the two will be electron donor  and the bottom  left product will be the electron acceptor  As you go down the tower you will release energy  As you increase the number of carriers = increase energy released  During photosynthesis light drives the electrons up the tower  ETC  This is a chain of mini electron towers  The first tower has a negative E’O  The first carrier is reduced and the electrons are transferred to the next carrier  Since the first tower is spontaneous, the energy is used to phosphorylate ATP  The net energy change of the complete reaction is calculated by the difference of reduction potentials of the primary and final acceptor  Increase nutrition= increase the goodness of the carriers  Electron Carriers  2 Classes o Coenzymes­ freely diffusible; can transfer electrons from one place to  another in a cell (NAD)  Nannies on the move taking care of the electrons o Prosthetic Groups­ fixed to the enzymes in the plasma membrane that  function  in membrane associated electron transport reactions  (cytochromes)  The star of +he electron carriers: NAD o NAD ­ nicotinamide adenine dinucleotide o NADP ­ nicotinamide adenine dinucleotide phosphate o NADH and NADPH­ good election donors and have a reduction  potential of ­0.32 V NOT A PART OF THE ETC!!!! ONLY BRINGS  ELECTONS!!!! o Coenzyme o Freely diffusible­ freely moving  Carries 2 e­ and 1H (the 1 H that is released) o NADP / NADPH works the same way except is involved in anabolism o  LIKE THE CURRENCY EXAMPLE, THE NAD+ HAS TO BE  RECYCLED!!!!!!!! (SHOWN BELOW)  (Ch 18)11.2­11.8  Electron acceptors for process  Electrons released during oxidation must have an electron dump (acceptor)  Exogenous: Final electron acceptor is from outside of the cell  Fermentation uses exogenous  Endogenous: Final electron acceptor is from inside the cell  Anaerobic respiration  Generation of ATP (MONEY )  Substrate­level phosphorylation o Used in fermentation  o ATP is synthesized during the steps of catabolism of an organic  compound o  Oxidative phosphorylation o Used in respiration o ATP is made by a proton motive force (ATP synthase) o  Photophosphorylation o Used by phototrophic organisms o Light drives the redox reactions that generate the proton motive force o  Respiration  Involves the use of an ETC  As electrons pass through the electron transport chain to the final electron  acceptor, a proton motive force (PMF) is generated and used to synthesize  ATP  2 types o Aerobic respiration  Final electron acceptor is oxygen o Anaerobic respiration  Final electron acceptor is an exogenous acceptor:  NO3­, SO42­, CO2, Fe3+, or SeO42­  Oxidative phosphorylation­ this is the primary producer of ATP  Fermentation  Endogenous electron acceptor o Pyruvate  Does not use ETC or PMF  ATP is made by substrate level phosphorylation  2/22/16 Aerobic Respiration­   process that completely catabolizes an energy source to CO2 using o Glycotic pathway o TCA cycle (Kreb’s Cycle) o ETC with O  a2 the final e acceptor  Produces ATP and recycles electron carriers  Production: o Max total yield of 32 ATP (If all goes well)  4 ATP from the oxidation of glucose (substrate level phosphorylation)  28 ATP from NADH and FADH being oxidized in the ETC (Oxidative phospholation) o ETC  Eukaryotes  Located in the membrane of the mitochondrion­ Christa   Prokaryotes  Located in plasma membrane  Some resemble mitochondrial ETC but many are different. o What is an ETC?  Series of electron carriers that work together to transfer electrons from  NADH and FADH2 to a terminal electron acceptor  Electrons flow from negative to positive reduction potentials  As they are transferred, energy is released to make ATP by oxidative  phosphorylation  THEREFORE, IT IS ONE BABY ELECTRON TOWER AFTER  ANOTHER!!!!!  NADH 2.5 ATP  FADH2 1.5 ATP  o What is so great about PMF?  Well, like the flagellum, PMF drives the phosphorylation of  ADPATP.   This is done by the smallest molecular motor known: ATP synthase  This motor sits at the end of the ETC and spins like a turbine attaching new phosphates to ADP by changing the conformation of its subunits  to accommodate ADP and phosphate.  As the electrons release energy in the ATC, protons are driven out of  the cell, this polarizes the cell and establishes your PMF  ATP synthase allows PMF (allowing the protons back end through the  ATP synthase), to drive the phosphorylation of ATP.   o Let’s look closer at the ATP synthase molecule   This motor is reversible  Big Picture o o BE ABLE TO CLACULET THE GLUCOSE YIELD AT ANY GIVEN  STEP!!!!!! SHE WILL TELL YOU IF SHE IS USING THE BRIDGE STEP  Entner­ Doudoroff Pathway o Used by some soil bacteria o Yield pyruvate and glyceraldehyde 3­P o THE KEY DIFFRENCE IS THE PRODUCT: 2­keto­3­deoxy­6­ phosphogluconate KDPG  So if you see this product get excited cause you got some points  o Product (when coupled with 2  half of Embden­Meyerhof)  1 ATP  1NADH  1 NADPH Anaerobic Respiration  Uses other electron carriers besides oxygen  Less energy yield because the difference in standard reduction potentials are not quite as  vast Fermentation  Takes the place of the absence of the exogenous electron acceptor o O not needed  Uses pyruvate­ endogenous (made inside the cell) o Reduces pyruvate o “Electron Dump”  Recycles electron carriers (notice a theme?) (this is why they ferment)  Forms only 2 ATP Via substrate level phosphorylation   Produces fermentation products o Classes  Ethanol­ bread, wine and beer  Lactic Acid  Homolactic­ cheeses, sour cream  Heterolactic­ pickles, buttermilk and spoilage of food  Mixed Acid­ 2.3 Butanediol  Propionic acid Microbial Growth and Reproduction (7.1, 7.3, 7.4, 7.6, 7.7)  Growth­ increase the number of cells o Usually study population growth rather than microbial growth  Binary Fission (two cells from one) o Cell elongation, cellular stuff increases proportionally o DNA is replicated and it is segregated o One cell  two cell= one generation  Growth curve o Observed in a batch culture  One place, One medium, One vessel, No addition of food,  Plotted as log of cell versus time o 4 Phases  Lag­ first starting out, the bacteria freaks out cause it might be different  So if you take your bacteria out of one medium and put it another  medium, then the bacteria must first orient itself before it can grow exponentially  The more difference the new medium is the longer the lag phase  will be   Log­ This is the exponential growth phase  Exponential  Maximal  Constant  Uniform and the healthiest cells  Stationary: when the cell number remains constant overtime  Stop reproduction  Death rate= reproductive rate  Reasons o Nutrient limitation o Limit oxygen o Toxic waste and cell accumulation o Critical population density  Starvation responses: o Morphological changes  Endospore formation  Decrease in size o Special starvation proteins  Increases crosslinks in the cell wall   DPS protein protects DNA  Chaperon protein prevents protein damage  Increases the length of this phase  Persister cells o Harder to kill o Increase the virulence of the bacteria  Death Phase  Lysis  Cant reproduce o Can be useful for absorbance and quantification 2/26/16 The mathematics of the growth curve  Generation time­ time needed to double in size (Doubling time)  Varies depends on the species and environment  Exponential growth­ cell number doubles with in a fixed time period (slope of the line) o Number of bacteria = 2  n = number of generations  Calculating number of generation between two populations: N 0 log N −log¿ o t n=3.3¿ o N tspecificnumber of bacteriaduringthelog phase o N 0intial populaiton o You don’t have to know how to derive it. o Just memorize this  Calculating generation time:  Example: 8 o Nt=1.0 x 10 o No= 5.0 x10 7 N 0 o log N tlog¿ n=3.3¿ o Therefore: 7 5.0x10 log1.0x10 −log¿ n=3.3¿ n=1−→only1generation Generation time =t/n2/1=2 hours/ generation=0.5 generations/ hour  Growth constant: k= 0.5 generations/ hour Measurement of Cell numbers:  Direct o Total cell counts – physical counting o Counting chamber o Electron counter­ problem is that you may count dead cells  Viable Cell counts­ counts the number of CFU’s o Plating technique­Gives underestimate o Membrane filter  Indirect o Dry weight o Turbidity  Spectrophotometer o 540­600 nm­ optimum absorbance for bacteria o Gives an over estimate because it counts the dead cells too.  Environmental Factors that affect cell numbers o Must be able to adapt  H2O availability  pH  temperature  O2  Pressure  Radiation  Extremophiles­ need extreme conditions in order to grow  Solutes and H2O activity o Water activity­ amount of water in the environment that is available to the  organism  01 = pure water = 1  Any type of solutes is unavailable to micro  Increase the solute concentration= lower the water availability o Adaptation  In Hypotonic solutions, bacteria use mechanosensetive channels in  membrane to allow solutes out which changes the osmotic surroundings  which will cause water to go out of the cell by osmosis  SOLUTES LEAVE FIRST THAT PULL WATER OUT  Hypertonic solutions­  Increase interval solute concentration with competitive solutes  More water comes into the cell  This explains why salt water is good for wounds, because the  bacteria in the wound unless they are halophiles or Extreme  halophile, they will undergo plasmolysis  NaCl  Nonhalophile=  can survive in little to no salt  Halophile­ can survive in little to a lot of salt  Extreme halophile­ can survive in a lot to a crap ton of salt.


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