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BSC 310 Exam 1 Study Guide

by: Caitlin Owens

BSC 310 Exam 1 Study Guide BSC 310

Marketplace > University of Alabama - Tuscaloosa > Biology > BSC 310 > BSC 310 Exam 1 Study Guide
Caitlin Owens

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This study guide includes lecture notes and notes from the readings for the first exam.
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This 29 page Study Guide was uploaded by Caitlin Owens on Tuesday February 9, 2016. The Study Guide belongs to BSC 310 at University of Alabama - Tuscaloosa taught by in Spring 2016. Since its upload, it has received 97 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 02/09/16
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O Kiddho 0396 Succindk m fumam rr and Nanihon o PM E FADHL A Moiecuif wi m ms nagging Poww Wan NNM AS 1 Y CSUH wa ATP MoH cuI Wm Of qmemkd Mm Wat flecmm Suw anc d hldmc1mq 3 IWt d1f d H1 inntr miwwonarmt Membrane and PaVHLipdhg 1 6mm Wmno chm View s qun vu ml Imnmp 33 f quotI 39 I x f I 4quot quotNVWSHWWWR W SCQUCnHai rmmom AI 31 E N e R 1 e mmavmfxdw To igvs tag fmfmm almost quot3 Phogppommn d 0 qtucoSf Phosphdc w fnLymc hcxokinast onforynqh ch Thai Wili allow 3 Dsomcma onrearrangcs Sugar molccuic WHO 61 1 0 b6 SPH39T i TU m0 3quotCana0 0 066 rmmime Unsth cxfrgonic gm WM 2quot 3 quot 4394 bffausc if 131M rm Sffp is mmv quotm cawfomsis i mos f gh MUMHJ LphogphWVMh on Symmemc Phosphowgar Hwbe JU biphOSPha i8 entra n d Wm gh kmast achww of tnumc yhospho rwrokinast CLEAVAL1ECDmpl m pnmmg pram by Praduimcj isomeric r riose Sugarsj gtle M 1 Vfraldthyoltaphosphan 43Pcah b6 056d in Subscqucm Humans I quot39 g Ha5mg and tSOWtH LMhD n Pmaucfg dihydraquc onc phOSPhaK and glxmramwvdt 39 397gt Pha89ha1tLL13m39mal Subs t mrt fW Chm Paw Phascah iso mtrasi 1 Wwiftul rim is Sipho ncd 0H b4 139va innrccnvtm We NHN iY 9510 1E STEPS W7 Chen 3 L muhd from W and ifs membOiim in The me H LNWHand 4 ATP Htr ldChch g phosphafc dCthrdenaSC Lafah dg camHon of want and Phomhowian cn of m3 in 7 qui m39ha SHPHHIST i3 fauambit and WOW WOW unfavorable rtam on to occur h 19 dthydngcnascahitjh WWW menu Wm quot F imquot wsgb39 an 6 mt rtPiactd by a fe mai WH 0 im39 m PN PN m m P 397 L I r M Subgm H lfVC PNSPhoqNHmH kihaSc amwzrs phosphorqiahun of M To Hwa phomnonuah on r39l 9 g vhogphomwm is onvtmd 0 wruvah mu 3 smum m Humans m cm 0 mm anoJmcr Kmasc phowmm am APP j 1 prletH C can tntcr armbu m anumbw qmways Microbiology Lecture 1 114 MICROBIOLOGY study of microorganisms MICROORGANISMS all single celled microscopic organisms plus viruses which are microscopic but not cellular Microbiology revolves around 2 themes 1 Understanding basic life processes a Microbes are excellent models for understanding cellular processes in unicellular and multicellular organisms 2 Applying that knowledge to the benefit of humans a Microbes play important roles in medicine industry and agriculture Importance of Microorganisms Oldest form of life largest mass of living material on Earth carry out major processes for biogeochemical cycles can live in places unsuitable for other organisms all other life forms require microbes to survive Microbial Cell Structure Eulltaryote contains nucleus and subcellular organelles Prolltaryote no nucleus does have nucleoid can have cell wall and membrane bacteria and archaea Properties of ALL Cells 1 Metabolism cells take up nutrients transform them and expel wastes a Genetic replication transcription translation b Catalytic energy biosynthesis 2 Growth nutrients from the environment are converted into new cell materials to form new cells 3 Evolution cells evolve to display new properties phylogenetic trees capture evolutionary relationships Properties of SOME Cells 1 Differentiation some cells can form a new cell structure such as a spore 2 Communication cells interact with each other by chemical messengers 3 Genetic Exchange cells can exchange genes by several mechanisms 4 Motility some cells are capable of self propulsion Microorganisms amp their environments They live anywhere there is life biosphere 100 150 lltm into earth 121 oC Populations Communities Ecosystems Diversity and abundances of microbes are controlled by resources and environmental conditionsex temp pH 02 chemical amp physical The activities of microbial communities can in turn control the chemical and physical properties of their habitat Impact of Microorganisms on Humans Control key ecosystem functions Agents of disease Key components of agricultural systems Key roles within food industry expanding to quotbiotechquot Microbiology began with the invention of the microscope Hooke 664 discovered fungi van Leeuwenhoek discovered bacteria Cohndiscovered endospores amp cotton stoppers Pasteur Koch 50 years Hesse agarjelly Petri dish Pasteur wine industry optical isomers defeat of spontaneous generation rabies vaccine Jenner smallpox 1 swan neck flask experiment Koch solid media pure culture Koch s postulates isolation of Microbacterium tuberculosis Beijerinck amp Winogradsky 50 years Beijerinck enrichment culture allows development of pure culture of many environmental microorganisms first to hint at presence of viruses Winogradsky chemolithotrophy nitrogen fixation Modern Era 6O years DNA as informational molecule of life Microbiology Lecture 2 119 Light Microscope RESOLUTION the ability to distinguish 2 adjacent objects as separate and distinct limit of resolution for light microscope is about 02 micrometers limits effective magnification to about ZOOOx bright field works great for pigmented cells but most bacteria are very difficult to see staining can be used to increase contrast simple stains differential stains specialty stains gram stain most common fluorescence microscopy UV light source and many times but not always fluorescence stains differential interference contrast Confocal Scanning Laser Microscopy couples a computerized microscope laser light soutce and fluorescent dye including green fluorescent protein Electron Microscope use electrons instead of photons to image cells and structures improves resolution from 02 micrometers to 02 nanometers Transmission Electron Microscopy TEM electromagnets function as lenses system operates in a vacuum enables visualization of structures at the moleculat level specimen must be very thin 20 60nm and be stained Scanning Electron Microscopy SEM specimen is coated with a thin film of heavy metal ex gold an electron beam scans the object scattered electrons are collected by a detector and an image is produced even very large specimens can be observed magnification range of 15x 100000x Cell Morphologies coccus rod spirilium spirochete budding amp appendaged bacteria filamentous bacteria know sizes bacteria range in size two giants epulopiscium fishelsoni thiomargarita namibiensis impact of size the higher surface area to volume ratio the faster diffusion can deliver remove compounds it is calculated that a cell must have a volume of atleast 0002 microlitersA3 sphere 015 microliter in diameter to contain the necessary proteins DNA ribosomes etc to function Membrane Structure phospholipids form the basic unit of the cytoplasmic membrane fluid mosaic model hydrophilic and hydrophobic groups membrane proteins Microbiology Lecture 3 121 Archaeal phospholipids isoprene units Archaeal membranes can be monolayer or bilayer Membrane Function permeability barrier prevents leakage and functions as a gateway for transport of nutrients into and wastes out of the cell protein anchor site of many proteins that participate in transport bioenergetics and chemotaxis energy conservation site of generation and use of the proton motive force watergtglycerolgttryptophangtglucosegtCl gtKgtNa for permeability How do cells acquire compounds with low permeability or against a concentration gradient Transporters Transport Systems 3 major classes of transport systems in prokaryotes 1 simple transport driven by the energy in the proton motive force 2 group translocation chemical modification of the transported substance driven by phosphoenolpyruvate 3 ABC system periplasmic binding proteins are involved and energy comes from ATP all require energy in some form usually proton motive force for active transport 3 transport events are possible 1 uniport transport a single molecule across the membrane 2 symport function as co transporters 3 antiport one molecule transports in and one molecule transports out Simple Transport well studied lac permease of Escherichia lactose is transported into Ecoli by the simple transporter lac permease a symporter H activity of lac permease is energy driven proton motive force although referred to as simple these should not be considered a simple tube as substrate interacts with protein conformational changes are associated with transport and the system is subject to regulation Group Translocation best studied system phosphotransferase system in Ecoli moves glucose fructose and mannose 5 proteins required energy derived from phosphoenolpyruvate how glucose is brought into the cell substrate level phosphorylation ABC ATP Binding Cassette System gt200 different systems identified in prokaryotes often involved in uptake of organic compounds sugars amino acids inorganic nutrientssulfate phosphate and trace metals typically display high substrate specificity contain periplasmic binding proteins specific to gram negative bacteria or anchored binding proteins gram positive bacteria in gram positive bacteria substrate binding protein is anchored to the exterior of the membrane Peptidoglycan active transport of solutes generates significant osmotic pressure on call membrane 30PS peptidoglycan is the rigid layer of the cell wall that resists this pressure peptidoglycan is a polysaccharide composed of N acetylglucosamine and N acetylmuramic acid and amino acid some D sshould be L amino acid and Lysine or diaminopimelic acid cell walls of gram positive and gram negative bacteria differ in structure Gram positive bacterial cell wall amp membrane presence of teichoic acid and lipoteichoic acidsanchor wall and membrane together lipids in the membrane composed of ribitol allows bacteria to have slightly negative charge on its exterior Gram negative cell wall amp membrane polysaccharide baclltbone more complex outer membrane outside of the peptidoglycan wall lipopolysaccharides extending from outer membrane can cause toxic shock in humans contains porins for transport 1500 daltons can pass through one AA1OOD cytoplasmic membrane peptidoglycan wall outer membrane lipopolysaccaride LPS structure O specific polysaccharide core polysaccharide lipid A Archaea Cell Walls S layers most common cell wall type among archaea consist of protein or glycoprotein paracrystalline structure also found in bacteria no peptidoglycan some contain pseudomurein murein is a pseudonym for peptidoglycan Prolltaryotes without cell walls Mycoplasmaspathogenic bacteria Thermoplasmaspecies of Archaea Cell Surface Structures capsules and slime layers capsules exclude particles polysaccharideprotein layer may be thick thin rigid flexible assist in attachment to surfaces biofilms protect against phagocytosis resist desiccation fimbriae filamentous protein structures enable organisms to stick to surfaces or each other pili filamentous protein structures typically larger than fimbriae assist in surface attachment facilitate genetic exchange between cells conjugation type IV pili involved in twitching motility and for some pathogens virulence Microbiology Lecture 4 125 Cell Inclusions carbon storage polymers Poly B hydroxybutyric acid PH B one of the research areas of my lab is to produce PHB from plant waste and then react with ethanol to produce a second generation liquid biofuel glycogen glucose polymer inorganic phosphate storage polyphosphates elemental sulfur storage sulfur globules magnetic storage inclusions magnetosomes Endospores a bit of a misnomer to call this an quotinclusionquot a cell within a cell highly differentiated cells resistant to heat harsh chemicals and radiation quotdormantquot stage of bacterial life cycle ideal for dispersal via wind water or animal gut only present in some gram positive bacteria structurally complex exosporium spore coat core wall cortex dewatered lower pH quaternary structure of DNA changed contains dipicolinic acid small acid soluble proteins SASPs enriched in Ca2 longevity is easily hundreds of years spore forming bacteria grown from 750 million year old glacier ice and 38 41 million years old in salts oceans also 20 30 million years ago in insects that have been fossilized by amber may be able to grow in ice and salt must repair DNA or have multiple copies of genomes Gas Vesicles confer buoyancy in planllttonic cells spindle shaped gas filled structures made of protein gas vesicles impermeable to water Flagellum different structure for gram negative and gram positive have rotor and stator Archaea also show flagella although proteins are different from those observed in Bacteria and they are driven by ATP Gliding a variety of Bacteria show gliding motility slim common in cyanobacteria Oscillatoria ex pringle can non gliding mutant Flavobacterium outer membrane is free to move transmembrane protein works like a ratchet with glide proteins to move membrane Microbial Taxis TAXIS directed movement in response to chemical or physical gradients chemotaxis response to chemicals phototaxis response to light aerotaxis response to oxygen osmotaxis response to ionic strength hydrotaxis response to water How Chemotaxis Worllts cell surface receptor senses compound measures gradients in time not space complex molecular machinery measure the rate of quothitsquot cells alternately quotrunquot and quottumblequot if rate of contact continues to increase runs become longer if rate of contact decreases runs become shorter tumbles quotpickquot a new direction at random if no attractant present random movement attractant present directed movement EUKARYA a domain of life characterized by celss containing a membrane enclosed nucleus and other subcellular organelles including mitochondria Golgi complex and endoplasmic reticula no longer microtubules and microfilaments cell structure NUCLEUS membrane bound region containing chromosomes visible under light microscope without staining enclosed by 2 membranes DNA is wound around histones not for Bacteria but some Archaea within the nucleolus site of ribosomal RNA synthesis Nucleus amp Cell Division unlillte Bacteria and Archaea most Eulltarya have 2 copies of each chromosomediploid many microbial eulltaryotes can be either diploid or haploid and may or may not show sexual reproduction the presence of more than one chromosome and the presence of 2 copies of each requires special forms of cell division vegetative cell division is called mitosis in Eulltarya chromosomes are replicated and partitioned into 2 nuclei results in 2 diploid daughter cells further specialization is required for sexual reproduction Meiosis reduces diploid number to the haploid number results in four haploid gametes upon gamete 2 fusion return to diploid state cell cell fusion rarely seen in Bacteria lilltely evolved in Archaea Mitochodria Hydrogenosomes amp Chloroplast all specialize in energy metabolism mitochondria respirationa and oxidative phosphorylation hydrogenosomes anaerobic respiration conversion of pyruvate to acetate C02 and H2 chloroplasts conversion of light energy to ATP and fixation of carbon chloroplasts mitochondria and hydrogenosomes suggested as descendants of ancient prolltaryotic cells endosymbiosis single origin evidence that supports idea of endosymbiosis mitochondria and chloroplasts contain DNA DNA is circular mitochondria and chloroplasts contain own ribosomes ribosome sequences align with those of living bacteria Eulltaryotic Mitochondria bacterial dimensions rod or spherical single circular DNA molecule 70 ribosomes a few per yeast cell to over 1000 in an animal cell surrounded by two membranes folded internal membranes called cristae contain enzymes needed for respiration and ATP production specifically in the matrix Eulltaryotic Hydrogenosomes similar size to mitochondria lacllt TCA cycle enzymes and cristae oxidation of pyruvate to H2 C02 and acetate found in various anaerobic protists and some parasitic forms microbial eulltaryotes that contain these carry out a strictly fermentative metabolism Eulltaryotic Chloroplasts chlorophyll containing organelle found in phototrophic eulltaryotes size shape and number of chloroplasts vary flattened membrane discs are thylalltoids lumen of the chloroplast is called the stroma which contains large amounts of RubisCO key enzyme in Calvin cycle Endosymbiosis idea that mitochondria and chloroplasts originated from bacteria mito chloro and hydro all contain their own genomes and ribosomes symbiotic relationship between respiratory and photosynthetic bacterial cells that received a stable and supportive growth environment inside the host which received an energy metabolism Other Major Eukaryotic Cell Structures internal membranes tubes and fibers also present in Lokiarchaeota Lokiarchaeota contain 17 of21 signature eukaryotic proteins internal membranes endoplasmic reticulum ER two types of ER smooth and rough rough contains attached ribosomes smooth does not golgi complex stacks of membrane distinct from but functioning in concert with the ER modifies products of the ER destined for secretion lysosomes membrane enclosed compartments that contain digestive enzymes that hydrolyze proteins fats and polysaccharides internal tubes and fibers microtubules 25nm in diameter composed of 0t and B tubulin function in maintaining cell shape in motility in chromosome movement and in movement of organelles microfilaments 7 nm in diameter polymers of actin function in maintaining cell shape motility by pseudopodia and cell division lntermediate filaments 8 12 nm in diameter llteratin proteins function in maintaining cell shape and positioning of organelles in cell Flagella amp Cilia confer swimming motility cilia are shorter than flagella structurally distinct from prolltaryotic flagella bundle of 9 pairs of microtubules surrounding the central pair in ciliaflagella dynein is attached to the microtubules and uses ATP causing tubules to slide past one another propel the cell using a rowing or whiplillte motion Microbiology Lecture 5 128 Essential elements as a percent of dry cell weight C 50 O 17 N 13 H 82 P 25 S 18 Trace elements Boron Cobalt Copper Iron Manganese Molybdenum Nickel Selenium Tungsten Vanadium Zinc Macromolecular composition of a cell Protein 55 Lipid 91 Polysaccharide 5 Lipopolysaccharide 34 DNA 31 RNA 205 NUTRIENTS elements and compounds required by cells for growth form matters MACRONUTRIENTS nutrients required in large amounts gt1 dry cell mass MICRONUTRIENTS nutrients required in trace amounts lt1 dry cell mass Carbon required by ALL cells typical bacterial cell is 50 carbon by dry weight major element in ALL classes of macromolecules same true for oxygen and hydrogen heterotrophs require organic carbon autotrophs use carbon dioxide Nitrogen N typical bacterial cell is 13 nitrogen by dry weight key element in proteins nucleic acids and many more cell constituents PhosphorusP synthesis of nucleotides nucleic acids and phospholipids Sulfur S sulfur containing amino acids cysteine and methionine vitamins lillte thiamine biotin and coenzyme A Potassium K required by enzymes for activity Magnesium Mg stabilizes ribosomes membranes and nucleic acids also required for many enzymes Calcium Ca helps stabilize cell walls in microbes plays key role in heat stability of endospores Sodium Na required by some microbes ron Fe lltey component of cytochromes and FeS proteins involved in electron transport Growth factors organic compounds required in small amounts by certain organisms vitamins amino acids purines pyrimidines Vitamins most commonly required growth factors most function as coenzymes Laboratory Culture of Microorganisms culture media nutrient solutions used to grow microns in the laboratory 2 broad classes 1 defined media precise chemical composition is known 2 complex media composed of digests of chemically undefined substances ex yeast and meat extracts liquid cells grown in test tube or flasllt mainly time shallten solid are prepared by addition of gelling agent agar or gelatin cells from colonies typically easier to detect contaminants selective media contain compounds that selectively inhibit growth of some microbes but not others differential media contain an indicator usually a dye that detects particular chemical reactions occurring during growth pure cultureculture containing only a single kind of microbe contaminants unwanted organisms in a culture microbes are everywhere sterilization of media is critical aseptic technique should be followed Microorganisms grouped into energy classes Chemotrophs amp Phototrophs Preformed organic carbon heterotrophs C02 autotrophs RubisCo key enzyme in cycle that fixes C02 Chemoorganotrophs uses OZ aerobe Chemolithotrophsdoesn t use OZ anaerobe Phototrophs produces OZ oxygenic doesn t produce OZ anoxygenic Bioenergetics Energy available in any reaction allows us to predict 2 things I will a metabolic reaction occur 2 wherewhen will a metabolic reaction ovvur free energy G is the energy released that is available to do work change in free energy during a reaction is referred to as AG 039 indicates standard conditions reactions with a negative AGO release free energy and are said to be exergonic reactions with positive AGO require energy and are said to be endergonic you can calculate free energy yield of a reaction from the free energy of formation Gfo the energy released or required during formation of a given molecule from the elements free energy formation of Hydrogen gas and Oxygen gas is O for the reaction AB CD AGO Gfo CD GfOAB C6H1206 602 l39 AGO6 23726 3944 9173 60 AGO 4232 23664 9173 AGO 37896 9173 28723 lltJ mol391 2NH4 202 N2 2H20 AGO 2 2372 2 O O 2 794 AGO 4744 588 AGO39 3156 lltJ mol Glucose oxidation AGO39 28723 lltJ mol391 Ammonium oxidation AGO39 3 56 lltJ mol391 Will either occur in nature Yes If glucose NH4 and 02 exist in an environment which metabolism will dominate Glucose Microbiology Lecture 6 22 Catalysts amp Enzymes a catalyst is a substance that lowers activation energy of a reaction increases reaction rate does not affect energetics or equilibrium of a reaction is not consumed during the reaction enzymes biological catalysts typically proteins some RNAs highly specific generally larger than substrate greatly reduce byproduct production many enzymes contain small non protein molecules that participate in catalysis but are not substrates Prosthetic groups Coenzymes Bind tightly to enzymes reversibly bound to enzymes Usually bind covalently amp permanently most are derivatives of vitamins eg heme group in cytochromes eg NADNADH Redox Reactions energy from oxidation reduction reactions can be used in synthesis of energy rich compounds ex ATP redox reactions occur in pairs electron donor the substance that loses electrons or is OXIDIZED in a redox reaction electron acceptor the substance that gains electrons or is REDUCED in a redox reaction 9can be written in half reactions When will a substance be an electron donor or acceptor The substance of a redox couple with a more negative Eo donates electrons to the substance of a redox couple with a more positive Eo so acceptor is the more positive 9Reduction potential Eo tendency to donate electrons expressed as volts V Reduction potential of an element or compounds tells us the likelihood of a substance to be an electron donors or acceptor TRU E This relationship depicted graphically is the redox tower reduced substance at the top of the tower donates electrons oxidized substance at the bottom of the tower accepts electrons the farther the electrons quotdropquot the greater the amount of energy released Direct utilization or donation at electron transport system 1 Enzyme reacts with e donor and oxidized form of coenzyme NAD 2 NADH and reaction product are formed 3 Enzyme reacts with e acceptor and reduced form of coenzyme NADH 4 NAD is released Glycolysis 2 main mechanisms for conservation of energy during metabolism 1 substrate level phosphorylation 2 oxidative phosphorylation dissipation of proton motive force coupled to ATP synthesis During glycolysis energy is conserved in the form of 2 net ATPs and 2 NADH TRUE glycolysis is a common pathway for catabolism of glucose Embden Meyerhof Parnas pathway anaerobic process with 3 stages Respiration NADH to electron transport and pyruvate to citric acid cycle 2 Fermentation glucose consumed 2 ATPs produced 3 if acid is released NAD regenerated by dumping electrons onto pyruvate fermentation products generated 9some harnessed by humans for food and beverage production for preservation Food Production through Fermentation Leuconostoc mesenteroides Lactobacillus brevis hererolactic bacteria associated with sauerlltraut and piclltle fermentations Propionibacteriaceae break down lactic acid into acetic acids and carbon dioxide swiss cheese Lactobacillus plantarum and Pediococus acidilactici homolactic bacteria used in traditional sausage mallting peperoni other Pediococus used in Lambic beer production malolactic fermentation of chardonnay Streptococcus thermophiles Lactobacillus bulgaricus homolactic bacteria used in yogurt production Acetobacter aerobic fermentation of produce vinegar acetic acid from ethanol Electron Carriers Flavin mononucleotide FM N accepts 2e and 2H donates only electrons adding an adenosine produces FAD Flavoproteins Cytochromes many different classes differ in electron potential designated a b c etc and have different varieties within those classes Non heme iron sulfur proteins have iron sulfur centers as prosthetic groups structure influences electron potential different proteins exhibit a wide range of reduction potentials Ferrodoxin is a common example Coenzyme Q a quinone Microbiology Lecture 7 24 Electron Transport ability to produce a gradient across the membrane generating proton motive force electrons enter chain form a primary electron donor electrons exit the chain by reducing the terminal electron acceptor 02 proton motive force is used by cells to synthesize ATP electron carriers are arranged within the membrane such that as electrons are transported protons are segregated from electrons 2 sources of H NADHor succinate and dissociation of water electron carriers are clustered into complexes V electrons can enter either complex I or both feed into q cycle electron flow from compounds with higher reduction potential to those with lower reduction potential complex V reduces the terminal electron acceptor protons are pumped out of the cell at complex I and IV and in the q cycle ATP Synthase uses proton motive force to take ADPP to make ATP 2 major domains F1 in cytoplasm F0 in membrane rotor spins with the passage of H FO ion translocation across the membrane causes c protein to rotate torque generated is transferred to F1 causing a transformational shift allowing ADP and Pi to bind relaxation causes synthesis of ATP Reversible allows the use of ATP to generate proton motive force only 2 rotor systems in life are ATP synthase and flagellum movemment Respiration C6H1206 602 6C02 6H20 ATP Pyruvate9Acetyl CoA through cleaving NADH and C02 acetogenic fermentation l ATP would be favored produces more ATP methanogenesis12ATP Citric Acid Cycle Citric acid cycle CAC pathway through which pyruvate is completely oxidized to C02 Per pyruvate molecule 3 C02 molecules released and 4 NADH I FADH2 and I GTP generated Plays a key role in catabolism and biosynthesis What to do with Acetyl CoA Make citrate and then stepwise remove carbons and energy until oxaloacetate is reformed lltnow where energy is conserved 5 CAC begins when the 2 carbon compound acetyl CoA condenses with the four carbon compound oxaloacetate to form the sis carbon compound citrate through a series of oxidations and transformations this six carbon compound is ultimately converted back to the four carbon compound oxaloacetate which then begins another cycle with addition of the next molecule of acetyl CoA 2 redox reactions occur but no C02 is released from succinate to oxaloacetate Succinate dehydrogenase and the process of FAD FADHZ feeds electrons directly into ETC at complex II in the Q cycle Acetyl CoA 3 NAD GDP FAD 2C02 3NADH FADH2 GTP substrate level phosphorylation 1 GTP ATP oxidative phosphorylation 3 NADH99 ATP 1 FADH292 ATP Total Conserved Energy Yield from Aerobic Respiration 38 ATP per glucose If we use 55lltJmol for ATP 2090 lltJmol is conserved AGO39 28723lltJmol 73 efficiency Citric Acid Cycle Overview Pyruvate is decarboxylated and energy is conserved as NADH and Acetyl CoA Energy is Acetyl CoA is used to synthesis Citrate from Oxaloacetate socitrate and a Ketoglutarate are decarboxlyated and energy conserved as NADH and the formation of Succinyl CoA which is used for a substrate level phoshphorylation Energy from further oxidation of Succinate is conserved as NADH and FADH2 and ultimately yields Oxaloacetate Rearrangements occur as necessary Metabolic Diversity Microorganisms demonstrate a wide range of mechanisms for generating energy Chemoorganotrophy fermentation aerobic respiration anaerobic resperation Chemolithotrophy aerobic respiration anaerobic respiration Phototrophy oxygenic anoxygenic Anaerobic Respiration the use of electron acceptors rather than oxygen ex nitrate N03 ferric iron Fe3 sulfate 8042 carbonate C033 certain organic compounds less energy released compared to aerobic dependent on electron transport to generation of a proton motive force and ATPase activity Chemolithotrophy uses inorganic compounds as electron donors ex H28 H2 F62 lll l4 typically aerobic but some anaerobic species are known uses ETC and proton motive force if autotrophic uses C02 as carbon source a few chemolithoheterotrophic bacteria are known Phototrophy uses light as energy source photoautotrophs use ATP for assimilation of C02 for biosynthesis photoheterotrophs use ATP for assimilation of organic carbon for biosynthesis with the exception of fermentation all microbial metabolic diversity is linked by its reliance on ETC and proton motive force for the conservation of energy Biosynthesis Sugars amp Polysachharides biosynthesis of glucose when sugar is absent from the environment reversal of glycolysis to make glucose o phosphate polysaccharides are synthesized from activated sugars this form for cell walls uridine diphosphoglucose adenosine for storage polymers in the absence of glucose it is synthesized from phosphoenolpyruvate gluconeogenesis Phosphoenolpyruvate can be synthesized from oxalacetate from CAC prolltaryotic polysaccharides are synthesized from activated glucose Adenosine diphosphoglucose for storage polymers cell walls from uridine diphosphoglucose pentoses are formed by removing one carbon from hexoses ribose 5 phosphate precursor to nucleotides reduction to deoxy occurs after production of nucleotide Biosynthesis Amino Acids amp Nucleotides Glutamate family Alanine family Valine Proline Pyruvate g ocKetoglutarate w Glutamine I Leucme I Arginine Gly 39ys39s Serine family 39 39 39 3Phos ho I cerate Glycme Citric acid cycle Aspartate family p g y Cysteine Asparagine Ph sph 39 o I Lysine enolpyruvate Aromatic family xa oacetate gt Methionlne Chorismate q gyriglilrl aelanme Threon39ne Erythrose4P from pentose phosphate Tryptophan Isoleucine pathway Figure 326 biosynthesis of amino acids and nucleotides often involves long multistep pathways often in families with branch points carbon sllteletons of amino acids come from intermediates of glycolysis or citric acid cycle ammonia is incorporated by glutamine dehydrogenase or glutamine synthetase and then can be transferred purine and pyrimidine biosynthesis are complex Biosynthesis Fatty Acids amp Lipids fatty acids are synthesized 2 carbons at a time 2 reductive steps ACP holds the growing fatty acid as it is being synthesized a complex transfer to and from CoA and ACP at priming steps the acid end represents the last acetyl from malonyl to be added Chapter1 Homework Characteristics of Achaea Bacteria Fungi and Viruses Bacteria have cell walls that contain peptidoglycan derive nutrients from organic or inorganic sources or conduct photosynthesis Archaea not typically associated with human disease found in extreme environments Fungi eukaryotic can be unicellular or multicellular Viruses can be seen only with an electron microscope cannot survive outside a host cell One of the first set of experiments to refute spontaneous generation was done in 1688 by Francesco Redi Which of the following statements regarding Francesco Redi s experiments is true The results of his experiment demonstrated that living organisms are derived from other living organisms In 1861 Pasteur conducted his now famous experiments using flasks with long necllts bent into an S shape Imagine that you are a scientist working in Pasteur s lab at this time You decide to tip the flasks so that broth enters the long S shaped necllt You then return the flask to its upright position Predict the most likely outcome of tipping one of Pasteur s S necked flasllts The broth would become contaminated with microbes because they were trapped in the neck Metabolism is a unifying characteristic of all cellular organisms Chapter 2 Homework A student observed a stained specimen of bacteria using bright field microscopy At 100x magnification there appeared to be only one cell in the field of view but at 1000x it was clear that there were two cells close together The ability to distinguish these two cells as separate entities is called resolution If a cell has a high surface to volume ratio there will be enough surface area to get the needed nutrients in to support cellular metabolism and the accumulated waste out If an E coli cell has a surface area to volume SV ratio of 45 and a Pelagibacter ubique has an SV ratio of 22 which cell will be able to exchange nutrients and wastes with the environment more efficiently Pelagibacter ubique because its cells are smaller Chapter 3 Homework Organic micronutrients are commonly called growth factors Fermentation occurs when there is no usable external electron acceptor like 02 available for respiration The fermentation products are made following glycolysis as a result of reactions that oxidize NADH so that NAD can be reused again in glycolysis How does the proton motive force lead to production of ATP Translocation of three to four protons drives the F0 component of ATPase which in turn phosphorylates one ADP into ATP Fermentation does not utilize the proton motive force Since glucose a hexose is the major source of energy for most prokaryotes why would they need to have pentose sugars available Pentose sugars are needed for nucleic acid synthesis A bacterium that lacks an arginine biosynthetic pathway would still be able to make proteins with arginine and grow only if arginine is supplemented into the growth medium TRUE Molebdenum is a cofactor for nitrogenase which means most nitrogen fixers require Mo to fix N9 TRUE Chapter 1 Book Outline GENOME living blueprint of an organism characteristics activities and survival of cell is governed by this PLASMID small circles of DNA in prokaryotes that typically contain genes that confer a special property on the cell Earth is 46byo and microbial cells first appeared 38 39bya all cells have descended from a common ancestral cell Earth s atmosphere only contained N2 and C02 for 2by only anaerobic microorganisms could survive phototrophic microorganisms evolved harvesting energy from sunlight cyanobacteriaoxygen evolving phototrophs began the process of oxygenating earth s atmosphere for multicellular organisms to evolve ECOSYSTEM all of the living organisms together with the physical and chemical components of their environment EXTREMOPHILES large group of Archaea and Bacteria whose collective properties define the physiochemical limits of life live in extreme environments History Hooke illustrates structures of molds Van Leeuwenhoek constructed simple microscopes first to see bacteria Cohn studied unicellular algae which led him to bacteria discovered endospores use of cotton for closing flasks and tubes Koch infectious disease agar plates tuberculosis postulates 1suspected pathogen must be present in all cases of the disease and absent from the healthy animals 2 suspected pathogen must be grown in pure culture 3 cells from pure culture of the suspected pathogen must cause disease in a healthy animal 4 suspected pathogen must be reisolated and shown to to be the same as the original Pasteur spontaneous generation Pasteur flask vaccines for choleraanthraxrabies Petri quotpetriquot dish standard tool for obtaining pure cultures Beijerinck enrichment culture technique microorganisms isolated from natural samples using highly selective nutrient and incubation conditions Winogradsllty proposed concept of chemolithotrophy oxidation of inorganic compounds to yield energy GENOMICS mapping sequencing and analysis of genomes fuels many advances in microbiology today Chapter 2 Book Outline Microscopes RESOLUTION ability to distinguish 2 adjacent objects as distinct and separate light microscopes used to examine cells at low magnification electron microscopes used to examine cells at high magnification Compound light microscope bright field phase contrast differential interference contrast darllt field fluorescence Gram stain gram positive bacteria appear purple gram negative bacteria appear pinllt because of differences in cell wall Phase amp darllt contrast improve image of unstained cells Differential interference contrast employs a polarizer in the condenser to produce polarized light cellular structures appear more 3D Confocal scanning laser microscope couples a laser to a fluorescent microscope useful for viewing thicllt specimens Transmission electron microscope used to examine cells at very high magnification and resolution only a thin section viewed Scanning electron microscope 3D imaging of cells specimen coated with a thin film of heavy metal electron beam then scans across only surface is typically visualized Small cells have more surface area relative to cell volume than do large cells so they have a higher surface to volume ratio SV ratio affects several aspects evolution growth rate nutrient exchange etc Smaller cells tend to grow faster than larger cells so smaller prolltaryotic cells have the capacity for more growth and faster evolution than larger eukaryotic cells Membranes Sterols are rigid and planar molecules that function to strengthen membrane of eukaryotic cells hopanoids serve a similar function in bacteria The lipids of Bacteria and Eulltarya use ester linkages to bond fatty acids to glycerol the lipids of Archaea contain ether bonds between glycerol and their hydrophobic side chains Archaeal lipids lacllt fatty acids hydrophobic side chains play the same functional role as fatty acids formed from multiple units of the 5 carbon hydrocarbon isoprene Cytoplasmic membrane of Archaea is formed from either glycerol diethers 20 carbon side chains or diglycerol tetraethers 40 carbon side chains Lipid monolayer membranes are extremely resistant to heat and are widely distributed among hyperthermophilic Archaea Membranes with a mixture of mono and bilayers are possible with some of the opposing hydrophobic groups covalently bonded and others not Membrane is a permeability barrier and an anchor for many proteins Proton motive force energy source responsible for many transport reactions swimming motility and biosynthesis of ATP Characteristics of transport systems 1 saturation effect if concentration of substrate is high enough to saturate the transporter which often occurs at very low substrate concentrations the rate of uptake becomes maximal and the addition of more substrate does not increase the rate this feature is essential for concentrating nutrients from very dilute environments 2 high specificity many transport proteins carry only a single kind of molecule whereas a few carry a related class of molecules 3 highly regulated specific complement of transporters present in cytoplasmic membrane of a cell is a function of both the nature and concentration of resources in its environment Transport proteins function to accumulate solutes against the concentration gradient Gram negative bacteria contain a region called the periplasm that lies between the cytoplasmic membrane and outer membrane periplasmic binding proteins membrane transporters and ATP hydrolyzing proteins make up the ABC transport system periplasm binding proteins have a high substrate affinity meaning they can bind their substrate even if it is only present at very low concentrations Cell Walls of Bacteria 96 RAM NEGATIVE consists of atleast 2 layers peptidoglycan cross Iinllt formed by a DAP peptide bond most of cell wall is composed of outer membrane second lipid bilayer that contains lipopolysaccharides consists of core polysaccharide and O specific polysaccharide in lipid A fatty acids are connected through amine groups from a disaccharide composed of glucosamine phosphate LPS functions as an anchor tying the outer membrane to peptidoglycan and it is toxic to animals Pathogens include Salmonella Shigella and Escherichia causing gastrointestinal issues due to toxic outer membrane components PERIPLASM gel Iillte space between outer surface of cytoplasmic membrane and outer membrane high concentration od proteins 96 RAM POSITIVE much thicker consisting of peptidoglycan90 cross Iinllt formed by short peptide interbridge contain teichoic acids embedded in cell wall and Iipoteichoic acids bound to membrane lipids peptidogchan polysaccharide composed of 2 sugar derivatives N acetylglucosamine and N acetylmuramic acid and amino acids including L alanine D alanine D glutamic acid and either L Iysine or DAP these join together to form a repeating structure called the glycan tetrapeptide Iong chains of peptidoglycan conntected by cross links of amino acids these glycosidic bonds are covalent and provide rigidity in only 1 direction the more cross linking the greater the rigidity Iysozyme can destryoy peptidoglycan present in tears saliva and other body fluids to protect against bacterial infection Mycoplasmas can form survive in nature without their cell walls Cell Walls of Archaea Contain psuedomurein similar to peptidoglycan made up of N acetylglucosamine and N acetyltalosaminuronic acid S layer paracrystalline surface layer consisting of interlocking molecules of protein or glycoprotein Fimbriae enables cells to stick to surfaces including animal tissues in the case of pathogenic bacteria or to form pellicles thin sheets of cells on a liquid surface or biofilms on solid surfaces fimbriae assist in disease process of salmonella gonorrhea and whooping cough Pili similar to fimbriae but are typically longer and only one or a few pili are present on the surface of the cell can be receptors for certain types of viruses function in conjugation and enabling adhesion of pathogens to specific host tissues that they subsequently invade Endospores During endospore formation a vegetative cell is converted into a nongrowing heat resistant and light refractive structure 3 steps activation germination outgrowth Endospore core contains small acid soluble spore proteins that bind tightly to DNA in the core to protect from potential damage from UV radiation dessication and dry heat Sporulation is an example of cellular differentiation and requires differential protein synthesis Flagellum functions to push or pull the cell through a liquid medium Bacteria polar flagellation flagella attached at one or both ends of a cell peritrichous flagellation flagella are inserted at many locations around the cell surface movement through a rotary motor composed of rotor and stator rotor central rod and the L P C and MS rings collectively these structures make up the basal body stator consists of Mot proteins that surround the basal body and function to generate torque energy required for rotation comes from proton motive force proton movement across cytoplasmic membrane through the Mot complex drives rotation of the flagellum protons flowing through Mot proteins exert electrostatic forces on helically arranged charges on the rotor proteins attractions between and charges would then cause the basal body to rotate as protons flow through Mot proteins 9 1000 protons per rotation synthesis MSC ring Mot proteins P ring L ring early hook late hook filament 15 20 nm Filament Flagellin Outer membrane LPS Mot protein Periplasm Peptidoglycan Basal body Cytoplasmic Mot protein Fli proteins Mot protein membrane motor switch I I 2012 Pearson Education Inc 45 nm Archaea powered directly by ATP Giding motility gliding prokaryotes are filamentous or rod shaped cells and the gliding process requires that the cells be in contact with a solid surface allows a cell to exploit new resources and to interact with other cells mechanism tracks exist in thr peptidoglycan that connect cytoplasmic proteins to outer membrane glide proteins and propel the glide proteins along the solid surface glide proteins and the cell proper move in opposite direction Chemotaxis bacterial cells respond to temporal rather than spatial differences in the concentration of a chemical as they swim attractants and repellants are sensed by chemoreceptors membrane proteins that sense and bind the chemicals to begin the process of sensory transduction to the flagellum a type of sensory response Chapter 3 Book Outline CULTURE MEDIUM nutrient solution used to grow microorganisms 0 Defined Media prepared by adding precise amounts of pure organic or inorganic chemicals to distilled water so exact composition is known 0 Complex Media made from digests of microbial animal or plant products such as casein beef soybeans yeast cells or any highly nutritious substance nutritional composition not known exactly 0 Enriched Medium used for culture of nutritionally demanding microorganisms such as pathogens starts as complex medium then additional substances such as serum or blood are added 0 Selective Medium contains compounds that inhibit growth of some microorganisms but not others available for isolation of certain pathogens 0 Differential Medium indicator typically dye is added which reveals a color change whether a particular metabolic reaction has occurred during growth useful for distinguishing bacteria ASEPTIC TECHNIQUE series of steps to prevent contamination during manipulations of cultures and sterile culture media Energy Classes Energy yielding rxns are a part of metabolism called CATABOLISM set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions Chemoorganotroph use organic chemicals energy is conserved through the oxidation of compounds conserved energy is trapped in the cell in the form of energy rich ATP bonds Chemolithotrophs produce energy from oxidation of inorganic compounds use C02 as carbon source Heterotroph cell carbon obtained from some organic chemical Autotroph uses C02 as carbon source primary producers because they synthesize new organic matter from C02 ENERGY ability to do work Exergonic rxns release energy and endergonic rxns require energy Gfo is the free energy of formation energy released or required during formation of a given molecule from the elements 0 Gfo of elements in electrically neutral form is O o Gfo for compounds is not 0 for most it is negative because compounds tend to form spontaneously from their elements which releases energy AGO is a reasonable estimate of free energy AG occurs under actual conditions 0 AG AGO39 RTan Free energy only calculates energy releasedrequired but not rate of rxn ACTIVATION ENERGY energy required to bring all molecules in a chemical reaction into the reactive state 0 Catalyst lowers activation energy of rxn thereby inc rxn rate not consumed or transformed o Enzyme biological catalysts enzyme combines with reactant substrate forms enzyme substrate complex reaction proceeds product released and enzyme returned to original state 0 Coupling energy requiring rxn run with energy yielding rxn like hydrolysis of ATP so overall rxn proceeds with free energy change that is either or near 0 REDOX RXNS 0 An oxidation is the removal of an electron a reduction is the gain of an electron for any substance oxidized another must be reduced 0 Reduction potential Eo inherent tendency to donate or accept electrons 0 Reduced substance whose E0 is more negative donates electrons to oxidized substance whose E0 is more positive 0 H2 is an excellent electron donor 02 is an excellent electron acceptor ATP 0 Prime energy currency in all cells generated during exergonic reactions and consumed in endergonic reactions 0 Energy required for synthesishydrolysis of ATP is 32kJmol Coenzyme A o Derivatives contain thioester bonds upon hydrolysis these yield sufficient free energy to drive the synthesis of an energy rich phosphate bond 0 Important to the energetics of anaerobic microorganisms whose energy metabolism depends on fermentation Fermentation amp Respiration o Fermentation form of anaerobic catabolism in which an organic compound is both an electron donor and acceptor o Respiration form of anaerobic or aerobic catabolism in which electron donor is oxidized with 02 or similar as terminal electron acceptor o More ATP produced in respiration but fermentation can supply enough energy for organism to survive Glycolysis breallts down glucose into pyruvate o Substrate level phosphorylation used in fermentation ATP synthesized directly from energy rich intermediated I Glucose phosphorylated by ATP yielding glucose 6 phosphate9isomerized phosphorylated split by aldolase converted to glyceraldehyde 3 phosphate 2 Production of NADH ATP amp Pyruvate 2 redox reactions oxidize 2 molecules of glyceraldehyde3 phosphate to 13 bisphosphoglyceric acid ATP synthesized when I molecules of 13 bisphosphoglyceric acid converted to 3 phosphoglyceric acid 2 each molecule of phosphoenolpyruvate converted to pyruvate a 2 ATP consumed amp 4 ATP synthesized net is 2 ATP per molecule of glucose fermented O 3 Redox Balance amp Production of Fermentation Products NADH reoxidized to NAD which allows earlier reactions of the pathway to continue Oxidative phosphorylation used in respiration ATP synthesized at expense of proton motive force Electron Carriers O NADH dehydrogenases flavoproteins iron sulfer proteins cytochromes quinonesnon protein electron carrier9oriented in the membrane such that as electrons are transported protons are separated from electrons arranged in order of increasingly more positive reduction potential with the final carrier in the chain donating electrons plus protons to a terminal electron acceptor such as 02 To initiate process 2 e and 2 H enter the ETC from NADH through NADH dehydrogenase Proton motive force separation of H amp OH electrochemical potential and difference in pH across the membrane cause it to be energized drives ATP synthesis transport reactions flagellar rotation and other energy requiring reactions in the cell Characteristics of all ETCs 1 carriers arranged in order of increasingly positive reduction potential 2 alternation of electron only and electron plus proton carriers in chain 3 net result is reduction of terminal electron acceptor and generation of pmf Complex V each complex consists of several proteins that function as a unit 0 0 Complex I NADH oxidized and quinone reduced Complex II bypasses Complex and feeds electrons from FADH2 directly into quinone pool called succinate dehydrogenase complex because succinate is oxidized fewer protons pumped per 2e that enter because of more positive reduction potential so reduces ATP yield by 1 per 2e consumed Complex bc1 complex present ETC of almost all organisms that respire functions to move e from quinones to cyctochrome c shuttle to transfer e to complex IV in periplasm Complex IV functions as terminal oxidase and reduces O2 to H20 in the final step of ETC also pumps protons to outer surface of membrane increasing strength of pmf Qcycle allows 2 additional H to be pumped to the outer surface of the membrane ATP synthaseATPase O O O F1multiprotein complex that sticks into cytoplasm and carries out ATP synthesis F0 membrane integrated component that carries out ion translocating function F1 amp Fo act as 2 rotary motors steps of ATPase 1 Movement of H through Fointo cytoplasm coupled to rotation of c proteins 2 1 Generates torque that is transmitted to F1 via coupled rotation of YE subunits 3 Rotation causes conformational changes in B subunits of F1 and allows binding of ADPPi 4 ATP synthesized when B subunits return to original conformation ATPase is reversible net result would be generation of not dissipation of pmf 0 Some forms of transport are powered by energy from prmc rather than directly from ATP so reversibility would be beneficial in those cases Citric Acid Cycle pathway by which pyruvate is oxidized to C02 plays a role in energy conservation amp biosynthesis


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