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Microbiology Final Review of All 4 Exam Topics

by: Mallory Ivy

Microbiology Final Review of All 4 Exam Topics BSC 310

Marketplace > University of Alabama - Tuscaloosa > Biology > BSC 310 > Microbiology Final Review of All 4 Exam Topics
Mallory Ivy
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These flashcards cover all the key terms from previous exams (for the cumulative portion of the exam) as well as more detailed terms for the material we just learned including viral diversity and g...
Dr. Olson
Microbiology, capsomeres helical icosahedral complex envelopes replication recognition attachment entry uncoating production of new viral components single double stranded DNA RNA positive-sense negative-sense ssRNA bacteriophage assembly egress, recombinat
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This 944 page Bundle was uploaded by Mallory Ivy on Monday May 2, 2016. The Bundle belongs to BSC 310 at University of Alabama - Tuscaloosa taught by Dr. Olson in Spring 2016. Since its upload, it has received 58 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 05/02/16
3 Domains of Life 1a Archaea, Eukarya, and Bacteria 1b (9+2) structure 2a describes structure of cilia and flagella; 9 pairs of microtubules surrounding a central pair 2b ABC Transport System 3a -ATP-binding cassette -Three components: substrate-binding protein/periplasmic binding, membrane-integrated transporter, and ATP-hydrolyzing protein -high-substrate affinity -found in both Gm- and Gm+ 3b amphitrichous 4a tufts of flagella at both poles of organisms 4b Archaeal Flagella vs. Bacterial 5a -uses several proteins unrelated to flagellin -uses ATP rather than PMF 5b archaeal membranes 6a -contain ether bonds between glycerol and hydrophobic side chains -side chains are repeating subunits of isoprene -composed of glycerol diethers and phytanhyl groups (20C)(bilayer) or diglycerol tetraethers and biphytanyl groups (monolayer) 6b autoclave 7a large, pressurized chamber using moist heat; used for sterilization 7b bond energy 8a anhydride > thioester > ester example compounds: phosphoenolpyruvate (anhydride) > ATP (2 anhydride and one ester bond) 8b Bright-Field Microscopy 9a only for organisms with pigmentation that sets them apart from the background 9b capsule 10a -tight matrix that blocks out small particles like stains -often stained with India ink most are firmly attached to cell wall 10b catabolism 11a breaking down; energy- yielding reactions 11b coenzyme 12a non-protein components of enzymes -ex: nicotinamide 12b cofactor 13a inorganic compounds that aid enzymes 13b complex media 14a uses digests of microbes, animals, or plants or their products -exact composition is unknown 14b Components of Flagellar Rotary Motor 15a rotar moves; includes central rod and rings stator is static; includes Mot proteins 15b Confocal Scanning Laser Microscopy 16a -laser source and fluorescent microscope -3D image with only one plane in focus at one time -layers can be assembled to give 3D image 16b conjugation 17a process by which bacteria exchange genetic information 17b Dark-Field Microscopy 18a -uses light that reaches specimen from only the sides -light is scattered by the specimen making it appear light on a dark background 18b defined media 19a Exact composition is known 19b diaminopimelic acid (DAP) 20a amino acid analog found in PG 20b Differential Interference Contrast Microscopy (DIC) 21a -produce polarized light in a single plane and goes through a prism -differences in the refractive indices of the material affect the rejoined two beams of light causing interference which enhances cell structures 21b differential media 22a uses and INDICATOR to reveal whether a particular chemical reaction has occured 22b Differential Stains 23a shows different types of cells in different colors -ex: Gram stain 23b dipicolinic acid 24a in core of endospore helps push out water alongside calcium ; appears necessary in spores but not in vegetative cells 24b endergonic reaction 25a requires energy input delta G is positive 25b Endospore Formation and Germination 26a 1. activation: usually heating at an elevated temperature 2. germination: loss of resistance to heat and chemicals and refractile nature 3. out grow: visible swelling due to water uptake and synthesis of RNA, DNA, protein 26b endospores 27a -highly differentiated cells that are highly resistant to heat, chemicals, and radiation -dormant -very refractile 27b Endospore Structure 28a 1. exosporium- outermost thin layer of protein 2. spore coat- multiple; within the exosporium with spore-specific proteins 3. cortex- loosely cross-linked PG 4. core- contains core wall, membrane, cytoplasm, cell components including dipicolinic acid 28b endosymbiont hypothesis 29a -chloroplasts, mitochondria, and hydrogenosomes are likely descendants of once free-living bacteria -each has its own genome and ribosomes, genetically similar rRNA to bacteria 29b energy storage polymers 30a glycogen, poly-β- hydroxybutyrate, and elemental sulfur 30b enriched media 31a adds additional nutrients such as BLOOD or SERUM to a complex base 31b Essential cations and anions for most organisms 32a potassium, magnesium, calcium, and sodium 32b essential nutrients for all organisms 33a Selenium, Nitrogen, Carbons, Hydrogen, Oxygen, Phosphorous, Sulfur (SeN CHOPS) 33b ester linkages 34a bacteria and eukarya have ester linkages between the fatty acids and glycerol 34b eukaryotic flagellar movement 35a propel in whip-like motion -occurs to microtubules sliding against one another; dynein uses ATP to drive motility 35b Ferdinand Cohn 36a founder of bacteriology 36b Ferric 37a F^3+ (threesome? ICK!) 37b free energy 38a -energy available to do work -designated by a G 38b Functions of Cytoplasmic Membrane 39a -permeability barrier -protein anchor -energy conservation 39b gelling agent 40a solidifies liquid cultures 40b genome 41a entire complement of an organism's genes 41b Germ Theory of Disease 42a diseases can be caused by microorganism that are too small to see by naked eye 42b glycan tetrapeptide 43a -PG subunits are connected to form a glycan tetrapeptide -contains N-acetylglucosamine, N- acetylmuramic acid and 4 of the following D-alanine, L-alanine, D- glutamic acid, lysine, and DAP (diaminopimelic acid) 43b glycogen 44a In addition to PHAs, glycogen is another form of intracellular C storage 44b Gm- Flagellar structure 45a includes flagellin, hook, L ring through outer membrane, rod extending through the basal body, P-ring through peptidoglycan layer, MS ring on the periplasmic side of the cytoplasmic membrane and a C ring on the cytoplasmic side of the membrane. between the MS ring and the C ring are Fli proteins. Surrounding the complex of Fli proteins and cytoplasmic membrane rings are MOT proteins. 45b Gram negative versus gram positive cells 46a gram negative- has thin PG and outer membrane gram positive- 46b Gram Stain 47a Gram positive stains purple and gram negative stains pink. 47b Group Translocation 48a -energy-rich organic compound drives the event -chemical modification driven by phosphoenolpyruvate -nonspecifc, Enzyme I --> HPr -- >specific Enzyme IIa --> Enzyme IIb--> Enzyme IIc embedded in membrane 48b heterotrophs 49a use organic carbon as source of carbon rather than CO2 49b hopanoids 50a bacterial structural analogs of sterols; used to strengthen membrane 50b hydrogenosomes 51a -found in cells without mitochondria that carry out a strictly fermentative metabolism -carries out oxidation of pyruvate to H2, CO2, and acetate 51b intermediate filaments 52a made of keratin proteins -maintain cell shape and position organelles in cell 52b Koch's Postulates 53a 1. suspected pathogen must be present in all cases of the disease and absent from healthy animals 2. suspected pathogen must be grown in pure culture 3. cells from a pure culture of the suspected pathogen must cause disease in a healthy animal 4. the suspected pathogen must be reisolated and shown to be the same as the original 53b layers of peptidoglycan are held together by _____ bonds 54a glycosidic bonds 54b lipopolysaccharide layer (LPS) 55a -in order from interior to exterior, consists of Lipid A (source of endotoxin), core polysaccharide, and O-specific polysaccharide (specific to species) 55b lophotrichous 56a tuft of flagella at one end of an organism 56b Louis Pasteur 57a -discovered optical isomers -spontaneous generation, technically termed germ theory of disease - pasteurization 57b LUCA 58a last universal common ancestor 58b lysozyme 59a cleaves bonds between PG saccharides 59b magentosomes 60a -found in several aquatic organisms that grow in low O2 environment 60b microfilaments 61a made of actin -maintain or change cell shape, motility, and in cell division 61b microtubules 62a -composed of alpha and beta tubulin -maintain cell shape, motility, chromosome movement during mitosis, and organelle movement within the cell 62b mitochondria 63a -location for respiration -double membrane -folded membranes called cristae with enzymes needed for respiration and ATP production -uses PMF to generate ATP 63b nicotinamide adenine dinucleotide (NAD+) 64a -coenzyme -transports two electrons and two protons at the same time -weak electron acceptor while NADH is a good electron donor -NAD+/NADH allows chemically dissimilar electron donors and electron acceptors to interact by acting as an intermediary 64b osmotaxis 65a response to ionic strength 65b outer membrane 66a -a second lipid bilayer in gram negative cell -out-facing side contains LPS layer -only in Gm- -contains porins 66b paracrystalline surface layer (S layer) 67a -consists of interlocking protein or glycoprotein -usually outermost layer of cell wall in archaea 67b peptidoglycan 68a -rigid layer responsible for the strength of hte wall -polysaccharide composed of N- acetylglucosamine and N-acetylmuramic acid -β (1,4) linkages between the two sugars -individual layers bound by peptide bonds 68b peripheral proteins 69a not membrane-embedded but remain associated often by an anchoring lipid tail 69b periplasm 70a lies between cytoplasmic membrane and outer membrane of Gm- bacteria 70b peritrichous 71a flagella attached anywhere and all over 71b Phase Contrast Microscopy 72a exploits subtle differences in refractive indices of water and cytoplasmic contents 72b pili 73a Function: -receptors for some viruses -facilitate conjugation -adhesion to specific tissues 73b poly-β-hydroxybutyric acid (PHB) 74a -common storage for carbon -due to size range, generically called poly-β-hydroxyalkanoates (PHA) -refract a great deal of light and numerous 74b porin 75a -found in outer membrane only -transmembrane protein that only small molecules can pass through 75b Properties of ALL cells 76a 1. metabolism 2. growth 3. evolution 76b Properties of SOME Cells 77a 1. differentation 2. communication 2. genetic exchange 4. motility 77b prosthetic groups 78a -bind tightly to enzymes, usually permanently -only association to one enzyme 78b pseudomeurein 79a -found in some methanogenic archaeal polysaccharide walls -backbone= N-acetylglucosamine and N-acetyltalosaminuronic acid -all AA are L-isomer -bonds are β(1,3) β(1,4) 79b quorem sensing 80a communication between bacteria that allow them to act together instead of individually 80b redox tower 81a -most negative Esub0' values at top -this reduced substance will most likely donate electrons to the [naturally] oxidized substance at the bottom -greater drop= greater released energy -deltaEsub0 prime is proportional to delta G sub0 prime 81b reduction potential 82a -tendency to be electron donor or acceptor, measured in volts in reference to a standard (hydrogen gas) -more negative= donor -more positive= acceptor 82b resolution 83a the ability to distinguish two adjacent objects as separate and distinct 83b RNA, DNA, or protein contribute most to the biomass of a cell! 84a protein; for this, there is a higher percentage of RNA than DNA but protein products outweigh both RNA and DNA 84b Role of Coenzymes in Redox Reactions 85a 1. enzyme I reacts with electron donor substrate and NAD+ 2. NADH and reaction product is formed 3. Enzyme II reacts with electron acceptor substrate and NADH 4. product and NAD+ are released 85b saturation gradient 86a can only go against gradient for so long until it requires too much energy the rate will level off 86b Scanning Electron Microscope (SEM) 87a -scanning the surface -3D image 87b selective media 88a INHIBITS growth of some microbes but not others 88b sigma factors 89a a protein needed only for initiation of RNA synthesis (thus transcription) 89b (simple) basic stains 90a methylene blue, crystal violet, and safranin 90b simple transport 91a -membrane-spanning transport protein; driven by proton motive force 91b slime layers 92a -less dense than capsules -pick up small molecules but not india ink -loosely attached to cell wall 92b Specialty Stains 93a specific for certain cells or certain parts of cells -ex: acid fast stains Mycobacterium's thick, waxy coating 93b teichoic acids 94a -embedded in cell wall that are covalently bonded to muramic acid --negatively charged phosphates are partly responsible for negatively charged membrane -bind calcium and magnesium -also covalently bound to membrane lipids are called lipoteichoic acid 94b thioester bonds 95a -found in compounds such as acetyl-CoA -actually better energy storage that outer two anhydride bonds in ATP 95b Transmission Electron Microscope (TEM) 96a -ultrathin section -requires staining -studies interior, 2D image 96b Type IV Pili 97a -assist cells in adhesion and provide twitching motility -gliding along surface through drag and retract method -requires ATP 97b Why are most eukaryotic genomes linear? 98a easier to access 98b 3 Characteristics of ALL electron carriers 1a 1. arranged in order of increasingly more positive (E0') reduction potential 2. alternate electron only and electron-plus-proton carriers 3. generation of PMF 1b acyl carrier protein 2a holds growing fatty acid during its synthesis 2b aerobic respiration 3a respiration with oxygen as the final electron acceptor 3b aminoacyl-tRNA synthetases 4a -requires ATP; links aminoi acids to its corresponding tRNA 4b anaerobic respiration 5a uses NO3-, Fe3+, SO4 2-, CO3 2-, or acetate instead of oxygen as the final electron acceptor; yields less energy than with aerobic respiration 5b archaeal RNA polymerase 6a archaeal cells has a single RNA pol that resembles eukaryotic RNA pol II and 11-12 subunits whereas eukaryotic cells have multiple RNA polymerases and 12+ subunits 6b ATPase in organism with ETC versus those without 7a with ETC- functions bidirectionally without ETC- functions unidirectionally 7b ATP synthase 8a 2 Components: -multiprotein (5) cytoplasmic complex called F1 that carries out ATP synthesis and a membrane integrated protein (3) component called F0 -uses 3 to 4 hydrogens per ATP 8b autolysin 9a enzyme that breaks the β-1,4 glycosidic bonds between N- acetylglucosamine and N- acetylmuramic acid in peptidoglycan and new peptidoglycan is inserted 9b bacterial promoters 10a -initiation sites on DNA recognized by sigma factors slightly upstream of gene -2 regions: Pribnow box and - 35 region 10b Bacterial Transcription Termination 11a GC-rich sequence and Rho protein 11b bacteriocin 12a protein produced by bacteria of one strain and active against those of a closely related strain -where we get most of our antibiotics 12b batch culture 13a organisms growing in closed system like a tube, flask, or Petri dish 13b Biosynthesis of Peptidoglycan 14a 1. transglycosylation= transglycosylases insert precursors (Bactoprenol) into growing cell wall and catalyze glycosidic bond formation 2. transpeptidation= final step that forms peptide cross-links 14b bonds between DNA strands 15a hydrogen bonds 15b bonds that hold DNA backbone together 16a phosphodiester bond 16b CAC has both bio_______ and bio_____ roles 17a synthetic and energetic 17b chaperones 18a -assist in folding/refolding partially denatured proteins -4 major ones in E. coli: Dna K, Dna J, Gro EL, Gro ES 18b chemostat 19a a continuous culture; growth and cell density are controlled 19b cytochrome 20a -proteins containing heme prosthetic groups -can form complexes with other cytochromes or with Fe- S proteins 20b deoxytriphosphates 21a sugar + base + 3 phosphate groups that are collectively attached to a growing chain using the 2 high energy anhydride bonds for the reaction 21b divisome 22a cell-division plane in center of the cell made by Fts Proteins 22b DNA Bacterial Polymerase Components 23a 5 subunits- β, β', α (2), ω, σ) however, sigma factor easily dissociates to find promoting region 23b DNA gyrase 24a removes supercoils ahead of DNA helicase which separates/unwinds the 2 strands 24b DNA helicase 25a -uses ATP to unwind dsDNA to expose short ss regions -separates strands in advance of replication fork 25b DNA ligase 26a joins strands/segments of lagging strand 26b DNA polymerase I 27a removes RNA primer and replaces it with DNA 27b DNA polymerase III 28a -replaces primase after primer is formed -has 2 sliding clamps and 1 clamp loader complex -cannot combine two separately synthesized stretches of DNA 28b DNA polymerases 29a -enzymes that catalyze the addition of deoxynucleotides -each species often has several with specific functions -cannot start a new chain 29b Fatty Acid Synthesis 30a -synthesized 2 C's at a time using acyl carrier proteins (ACP) which holds growing fatty acid -each C2 unit originates from malonate (C3) -low temperature environment results in short chain fatty acid whereas a high temperature results in a longer chain 30b fermentation 31a -anaerobic catabolism -organic compound is an electron donor and acceptor -uses substrate level phosphorylation 31b ferredoxin 32a Fe2S2 is an iron-sulfur containing protein that functions in electron transport 32b FtsA 33a -anchors FtsZ to cytoplasmic membrane -recruits other divisome proteins -related to actin 33b FtsI 34a -penicillin-binding protein that assist in PG synthesis 34b FtsK 35a -pulls 2 copies of chromosomes to each of their respective daughter cells 35b Fts Proteins 36a -filamentous temperature sensitive -found in all bacteria; archaea only have FtsZ -interact to form divisome 36b FtsZ 37a -forms membrane-associated ring in center of the cell -inhibited by nucleoid region 37b generation time equation 38a g= duration of exponential growth/ number of generations during exponential growth 38b glucogneogenesis 39a -synthesis of glucose -uses phosphoenolpyruvate (intermediate of glycolysis) and goes backwards 39b glycolysis 40a -breaks down glucose into pyruvate -anaerobic -3 stages: I + II all organisms; III- fermenting organisms only -net gain= 2 ATP 40b glycoxylate cycle 41a variation of CAC utilized when intermediates are siphoned off for other purposes; generates malonate to be made into oxaloacetate so that CAC can proceed 41b Growth Cycle 42a 1. lag phase 2. exponential growth phase (slope) 3. stationary phase (plateau) 4. death 42b heterocyst 43a a differentiated cell within cyanobacteria dedicated to N2-fixation 43b How ATPase works 44a -F1 + F0 are rotary motors -p+ move through F0 causing rotation of c proteins generating torque in F1 through rotation of γε subunits and results in conformational change of β subunits, allowing them to bind ADP + phosphate. Return to original conformation produces ATP. -synthesis: oxidative phosphorylation if PMF originates from respiration or photophosphorylation if it originates from photosynthesis 44b lipid biosynthesis 45a simple fats--> 3 glycerol Carbons are each "esterified" with a fatty acid phospholipid--> one C atom in glycerol has a phosphate group attached to it 45b Min proteins 46a -MinC and MinD accumulate at the poles -MinE forms in the center -ensures divisome only forms at cell center 46b Molecular Adaptations of Psychrophiles 47a -more alpha helices -cold shock proteins -more polar AA and less hydrophobic 47b MreB 48a -major shape-determining protein in Bacteria and likely archaea -forms spiral shaped bands just below the membrane and directs synthesis of new peptidoglycan (PG) -coccoid cells lack MreB gene indicating that coccoid cells are the 48b nitrogenase 49a -enzyme that catalyzes nitrogen fixation -2 protein components: dinitrogenase (iron and molybdenum aka FeMo-co) and dinitrogenase reductase (iron) -some nitrogenases use vandium and iron or only iron (latter is found in archaea) -irreversibly inactivated by O2 49b nitrogen fixation 50a -process of forming ammonia (NH3) from (N2) --NH3 is assimimilated into AA and nucleotides -not done by eukaryotes -energy-demanding; 8 electrons consumed (2 ATP consumed per electron so 16 ATP per N2) 50b nucleoside 51a nitrogenous base + sugar (no phosphate) 51b open reading frame 52a a start codon followed by codons and a stop codon in a single reading frame -considered a putative protein 52b operons 53a -multiple genes are transcribed together -only found in prokaryotes 53b optical density vs absorbance 54a OD is the amount of light passed through while absorbance is the amount of light scattered 54b origin of replication (OriC) 55a -bacteria have a single location on the chromosome where replication is initiated 55b oxaloacetate 56a binds to acetyl-CoA to begin citric acid cycle 56b oxidative phosphorylation 57a ATP synthesis that is driven by PMF produced during respiration 57b plate count methods 58a spread plate and pour plate; differ in that spread plate uses a greater volume of culture -goal is to get between 30-300 colonies 58b polycistronic mRNA 59a -mRNA encoding a group of cotranscribed genes that when translated creates several polypeptides 59b Polypeptide Structure 60a Primary- AA sequence Secondary- H bonds to form alpha helices and beta-pleated sheets Tertiary- interactions between R groups Quartenary- multiple ppc stabilized by disulfide bonds 60b polysome 61a multiple ribosomes can translate a single mRNA simultaneously 61b primase 62a RNA polymerizing enzyme that makes the RNA primer 62b primer 63a -nucleic acid molecule to which DNA polymerase can attach the first nucleotide -usually a short stretch of RNA -eventually removed and DNA poly I fills in missing nucleotides 63b primosome 64a helicase and primase complex that aids in replication process 64b products of the citric acid cycle 65a 1 pyruvate yields 3 CO2, 4 NADH, 1 FADH2, and 1 GTP 65b Promotors of Archaea and Eukarya 66a -TATA box -B recognition element (BRE) recognized by transcription factor B (TFB) -initiator element (INIT) recognized by TFB 66b Protein Synthesis 67a 3 steps: 1. initiation 2. elongation 3. termination 67b quinones (CoQ) 68a -non-protein electron carriers involved in ETC -hydrophobic -can accept 2 electrons and 2 protons but only transfer two electrons 68b redox enzymes that participate in ETC 69a -flavoproteins -cytochromes -NADH dehydrogenases -Fe-S proteins (Fe2S2=ferredoxin) 69b reduction potential 70a difference between 2 points on redox tower 70b replisome (6 components) 71a -complex of DNA pol III, helicase, primase, gyrase, single-stranded binding proteins, and tau proteins through which DNA is pulled during replication 71b respiration 72a -aerobic catabolism -compound oxidized with O2 -uses oxidative phosphorylation to produce ATP 72b Rho protein 73a binds to RNA and terminates transcription in bacteria 73b ribonuclease 74a removes archaeal spacers -only processing occurs for genes coding for rRNA and tRNA 74b ribosomes 75a -30S and 50S subunits in prokaryotes -30S recognizes tRNA, mRNA transcript, and initiation proteins then 50S subunit joins 75b RNA polymerase 76a -enzyme that carries out transcription -can initiate new strands on its own -transcribes genes on either strand of DNA -stops at transcription terminators 76b rRNA 77a creates 30S and 50S ribosomal subunits; has structural and catalytic (forms peptide bonds between AA of tRNA) roles 77b SecA Protein 78a binds proteins that are to be fully transported across membrane 78b Shine-Delgarno Sequence 79a found in untranslated region; aligns reading frame in bacterial RNAs 79b signal recognition particle (SRP) 80a -binds proteins that will be inserted into membrane -contains a signal protein and a small non-coding, not-to-be- folded RNA molecule 80b signal sequence 81a -marks proteins to be transported through membrane -usually have several (+) residues, central hydrophobic region, and more polar end region -keeps protein from completely folding -removed after transport 81b Start Codons 82a AUG; codes for modified methionine 82b Stop Codons 83a UAA, UAG, UGA 83b substrate-level phosphorylation 84a -ATP synthesized from energy-rich intermediates -[sugars] act as both electron donor and acceptor 84b supercoiling 85a more twisting of genome (-) form is predominant in nature (fewer turns) inserted or removed by topoisomerases 85b Tat system 86a -proteins that require cofactors but need to be secreted are folded inside cell (cofactors are difficult to find outside the cell) -TAT= twin arginine translocase -uses PMF for energy -TatBC carry protein to TatA which is the membrane transporter 86b tau protein 87a holds DNA pol III together and in place 87b Temperature Classes of Bacteria 88a psychrophile (optimal temperature= 4 degrees C) mesophile (OT= 39 degrees C) thermophile (OT= 68 degrees C) hyperthermophile (OT= 88 degrees C) hyperthermophile (OT= 106 degrees C) *yes, there are two types of hyperthermophiles 88b Ter site vs Tus proteins 89a termination (ter) sites recognized by Tus proteins, which block progress of the forks 89b tmRNA 90a -has both tRNA and mRNA character -free ribosome from mRNA lacking a stop codon 90b topoisomerase IV 91a cuts both strands to unlink 2 CIRCLES that were produced in replication 91b translocase 92a enzymes that transports proteins through and into cytoplasmic membrane 92b tRNA 93a carries anticodon that base pairs to an AA and mRNA codon -ssRNA with extensive secondary structure that creates a cloverleaf structure -anticodon loop and 3' acceptor end with 3 unpaired nucleotides 93b Type I versus Type II topoisomerase 94a Type I cuts one strand of DNA to either increase or decrease supercoiling and reseals whereas type II cuts both strands or cuts 2 loops at once 94b Types I-VI Secretion Systems 95a -Types I, III, IV, and VI require 1-step and have a channel through both membranes -Types II and V require 2 steps to move the protein through inner and outer membrane -Type III acts as a syringe 95b Types of Plasmids 96a -Resistance plasmids -Pathogenic -Bacteriocin producing 96b wobble 97a irregular base pairing at 3rd position of codon; allows for 64 codons to code for 22 amino acid 97b Yield of ATP in Fermentation vs Aerobic Respiration 98a fermentation yields 2 ATP while aerobic respiration yields 38 98b ZipA 99a -anchors FtsZ to cytoplasmic mebrane -related to tubulin 99b 454 System 1a DNA is broken into small fragments and attached to small beads. Each is placed into a well on a fiber-optic plate. DNA is amplified by PCR. Each time a base is added to the DNA strand, light is released and is measured in accordance to the nucleotide that was incorporated. 1b acidophiles 2a grow best below pH 5.5; often found in acidic thermal soils associated with volcanic activity 2b acidophilicity 3a dependent on cytoplasmic membrane stability; pH 2 above optima will cause cell to spontaneously lyse 3b activator 4a regulatory protein used in positive control; activator binding site can be several hundred base pairs upstream of the operon 4b activator protein helps RNA polymerase recognize promotor by either 5a changing DNA structure allowing the RNA pol to contact promotor more readily or can interact with RNA polymerase directly 5b aerobes 6a grow at full oxygen tensions 6b aerotolerant anaerobes 7a can tolerate and grow in the presence of O2 even though they cannot respire 7b alkaliphiles 8a -showing growth pH optima of 8 or higher; typically found in soda lakes and high- carbonate soils -some extremely alkaliphiles are also halophiles -some produce hydrolytic exoenzymes that are excreted from the cells; often added as supplements to laundry detergents to remove protein and fat stains 8b anaerobes 9a cannot respire O2 at all 9b antimicrobial agent 10a natural or synthetic chemical that kills or inhibits the growth of microorganisms 10b antimicrobial agent susceptibility assay in tubes 11a A series of tubes is inoculated with the test organism and a given amount of agent is added. After incubation, the tubes are scored for turbidity, and the MIC is the lowest concentration of agent that completely inhibits growth of test organism. 11b antiseptics 12a -aka germicides -chemicals that kill or inhibit the growth of microorganisms but are sufficiently nontoxic to animals to be applied to living tissues -some are also effective disinfectants 12b Attenuation 13a form of transcriptional control by early termination of mRNA synthesis; found in bacteria and archaea -not possible in Eukarya due to physical distance between transcription and translation 13b Attenuation in Tryptophan Operon 14a Leader sequence encodes leader peptide which contains tryptophan codons side-by-side. -If tryptophan is plentiful, the leader peptide will be synthesized and form a stem-loop, resulting in termination of transcription of remainder of operon. -If tryptophan is scarce, causes a stalled ribosome, which results in stem-loop formation that prevents termination allowing the remainder of the operon to be transcribed. 14b autoclave 15a sealed heating device that uses steam under pressure to kill microorganisms 15b autoinducer 16a specific signal molecule synthesized by the participating organism that freely diffuses across the cell envelope in both directions 16b catabolite repression 17a mechanism of global control that decides between utilizing different available carbon sources 17b Catabolite Repression Process on Lac Operon 18a When glucose is present, glucose siphons cAMP out of the cell. However, when glucose levels are low, cAMP is no longer sent out of the cell leaving it to bind to CRP. CRP forms a dimer when bound to cAMP and acts as a regulator. For the operon to be translated though, the repressor must be removed by the inducer (in this case, lactose). Lactose binds to the active repressor and thence removes it from the promotor site unblocking it for transcription. Both of these processes must occur for the lac operon to be transcribed. 18b catalase 19a converts hydrogen peroxide to water and oxygen 19b Caulobacter Differentiation 20a Swarmer= free swimming cells; cannot divide or replicate their DNA. Stalked (attached) cells- lack flagella and are attached to a surface via a stalk with a holdfast reproductive stage. Regulated by GcrA, CtrA, and DnaA i.GcrA is critical for cell division into differentiated cells and thus is active in the daughter cells only ii. CtrA is very active in flagellation 20b chromosomal islands 21a extrachromosomal elements that are not plasmids or integrated viruses; contains clusters of genes for specialized functions that are not needed for simple survival -ex: megnetosome island of Magnetospirillum -some carry a gene encoding an integrase enzyme to move it into a chromosome -target site is duplicated upon insertion; an intact tRNA gene is regenerated while the chromosomal island is inserted in place of what was to be another tRNA gene 21b -cidal agents 22a kill the microorganisms; bacteriocidal, fungicidal, etc. 22b Closed vs. Draft Genome 23a gaps in the sequence annotation is found in a draft genome whereas a closed genome has no gaps 23b compatible solutes 24a -solute that does not inhibit cellular processes in any significant way but allows halophiles to maintain a positive water balance -typically highly water-soluble organic molecules such as sugars, alcohols, or amino acid derivatives -maximum level of compatible solute is a genetically encoded characteristic 24b Connecting Unknown protein with a particular gene from genomic DNA 25a oligonucleotide probes or primers can locate the gene encoding the protein and then identify the gene after sequencing the DNA 25b Connecting unknown protein with particular gene from 2D gel system 26a 1. elute protein from gel and sequence a portion, or 2. identify protein by use of mass spectrometry 26b core genome 27a core genome is a genome found in all strains of a given species 27b corepressor 28a substance that stops enzyme synthesis (ex: arginine) 28b Culture Techniques for Aerobes 29a forced aeration is necessary so the flask or tube must be vigorously shaken or have sterilized air bubbled into the medium through a fine glass tube or porous glass disk 29b Culture Techniques for Anaerobes 30a -Bottles or tubes filled completely to the top with culture medium and fitted with leakproof closures and a reducing agent can remove any remaining O2 -obligate anaerobes can incubate in tubes or plates in a glass jar that is flushed with an O2- free gas or fitted with an O2 consumption system 30b cyclic AMP receptor protein (CRP) 31a activator protein responsible for catabolite repression; only acts when bound to cyclic adenosine monophosphate (cAMP) 31b cyclic di-guanosine monophosphate 32a another regulatory nucleotide; provides physiological changes and expression of virulence genes necessary for biofilm formation 32b decontamination 33a physical method of control that consists of treatment of an object or surface to make it safe to handle; simply removes present organisms 33b depth filter 34a -fibrous sheet or mat made from random array of overlapping paper or borosilicate fibers -important in biosafety applications such as in safety hood 34b Detecting Horizontal Gene Flow 35a 1. presence of genes that encode proteins typically found in distantly related species 2. presence of a stretch of DNA whose GC content or codon bias differs significantly from the rest of the genome 3. however, as more genomes are sequenced, using horizontal gene flow as an explanation can be nulled 35b diauxic growth 36a result of catabolite repression; cells grow first on preferred C source. Once first source is depleted, the organism undergoes a lag phase before resuming on another C source. 36b Difference between first-, second-, third-, and fourth-generations of DNA Sequencing 37a First generation- Sanger Dideoxy Method; read length 700-900 bases Second generation- 454 pyrosequencing; very large number of samples are sequenced side-by-side in the same machine requiring miniaturization and increased computing power Third generation- sequencing of single molecules of DNA based on microscopy (HeliScope Single Molecule Sequencer) or nanotechnology (Pacific Biosciences SMRT) Fourth generation- "post light sequencing" meaning optical detection is no longer used; ion torrent method or nanopore technology 37b Different Classes of Autoinducers 38a acyl homoserine lactones (AHLs), autoinducer 2, short peptides 38b differentiation in bacteria 39a formation of endospores in Gm+ Bacilli and formation of two cell types in Gm- Caulobacter (flagellated cells and those stuck to a surface) 39b disc assay for antimicrobial agent susceptibility 40a Known amounts of an antimicrobial agent are added to filter-paper discs and discs arranged on surface of uniformly inoculated agar plate. The zone of inhibition is proportional to the amount added to the disc, solubility of the agent, diffusion coefficient, and the overall effectiveness of the agent. Used to test clinically isolated pathogens for their antibiotic susceptibility. 40b disinfectants 41a -chemicals that kill microorganisms but not necessarily endospores -used on inanimate objects -important to infection control in medical settings 41b disinfection 42a physical method of control that specifically targets pathogens although it may not eliminate all microorganisms; actually kills or inhibits growth 42b DNA-binding protein 43a -interact with DNA in a sequence-specific manner, usually at inverted repeat, either act as enzymes for a specific reaction on DNA or can either block or activate transcription -does not require formation of stem-loop structure -homodimeric each divided into domains; each subunit of the dimer binds to one of the inverted repeats, thus, as a whole, the dimer binds to both DNA strands 43b effect of methylation on methyl-accepting chemotaxis proteins 44a methylated MCP is more sensitive to repellants and no longer responds to attractants and vice versa; allows cell to continue sense environment 44b effectors 45a Inducers and corepressors collectively are called effectors. Effectors assert allosteric control on their repressors. 45b emergent properties 46a behavior or properties of a particular organism that were not obvious from the original observations 46b Estimated lower limit of number of genes possible for a viable cell 47a 250-300 genes 47b Evidence that chromosomal islands have foreign origin 48a 1. extra regions are often flanked by inverted repeats suggesting they were inserted by transposition 2. the base composition and codon bias often differ significantly from that of the genome proper 3. found in some strains but not others 48b example of regulatory nucleotide 49a cyclic adenosine monophosphate and cyclic di-guanosine monophosphate (see the trend here?) 49b extreme halophiles 50a grow optimally at NaCl concentrations between 15 and 30% and are often unable to grow at all at NaCl concentrations below this 50b facultative aerobes 51a under appropriate nutrient and culture conditions they can grow in the absence of O2 but prefer to grow with O2 51b Feedback Inhibition 52a Works by allosteric enzymes; temporarily shuts off reactions in an entire biosynthetic pathway due to excess end product inhibiting an early enzyme in the pathway 52b filter sterilization 53a -used for heat sensitive liquids or gases -depth filter, membrane filter, and nucleopore filters 53b Finding a Functional ORF 54a 1. locate start and stop codons 2. most functional ORFs must be longer than 300 nucleotides but some are shorter. --> locate potential ribosome-binding sequences 3. codon bias 4. compare to similar genes in other organisms (protein homology) 54b Fourth-Generation DNA Sequencing 55a no longer uses optical detection; release of protons versus light 55b gene family 56a genes that are related in sequence to one another as a result of a common evolutionary origin 56b Genes and Proteins involved with Nitrogen Fixation (6) 57a -NifA- positive regulator for expression of nif genes -NifL- negative regulator for expression of nif genes -NtrC- active when little ammonia is present; promotes transcription of NifA (the positive regulator) -PatS- peptide produced by heterocysts that diffuses in both directions from the cell preventing the formation of more heterocysts -NtcA- transcriptional regulator that functions when α-ketoglutarate levels are high and activates transcription of hetR gene -HetR gene- controls heterocyst formation and genes to eliminate O2 and express nitrogenase 57b genomics 58a mapping, sequencing, analyzing, and comparing genomes 58b global control systems 59a regulatory mechanisms that respond to environmental signals by regulating expression of many different genes; includes flagellar genes 59b Good buffer 60a -a suite of organic molecules called Good buffers have been designed, each of which function best within a specific pH range, thus one buffer will be added to culture medium for an alkaliphile while another buffer will be used for an acidophile's culture medium -Good buffers are separate from potassium phosphate and sodium bicarbonate, which are used for neutrophiles 60b Growth Regions of Thioglycolate Broth 61a -obligate aerobes grow at the top -facultative aerobes grow throughout the tube but best near the top -microaerophiles grow near the top but not right at the top -anaerobes only grow near the bottom 61b halotolerant 62a organisms that can tolerate some level of dissolved solutes but grow best in the absence of the added solute 62b heat shock 63a another global control network that counteracts heat shock by heat shock proteins which help calls recover from temperature stress and damage; can be caused by heat, chemical exposure, and UV radiation 63b Heat Shock Regulation in E.coli 64a In low temperature, the chaperone DnaK binds to an alternative sigma factor (ribosomal polymerase H) RpoH which will be degraded. However, in high temperatures, RpoH is released while DnaK aids in refolding denatured proteins. RpoH is free to transcribe heat shock genes. 64b helix-turn-helix structure 65a A DNA-binding protein domain that consists of two helices connected by a "turn". The first helix is the recognition helix that interacts specifically with DNA. The second helix stabilizes the first. The turn is a short sequence of three AA, the first of which is typically a glycine. -ex: found in lac and trp repressors 65b Heterocyst Formation 66a -Initiated by low levels of nitrogen exhibited by elevated levels of α-ketoglutarate -These elevated levels activate NtcA which activates transcription of hetR gene (controls heterocyst formation and genes to eliminate O2 and express nitrogenase) -PatS peptide produced in heterocysts diffuses into adjacent cells 66b Heterocysts 67a cells where N2 fixation occurs, arise via monitoring of external conditions and cell-to-cell signaling 67b Hfq 68a RNA chaperones that help small RNA molecules to maintain their correct structure 68b homolog 69a genes related in sequence to an extent that implies common genetic ancestry; includes orthologs and paralogs 69b How do alkaliphiles manage bioenergetics when surrounded by such an H+ poor environment? 70a - use of sodium rather than H+, thus a sodium motive force versus a proton motive force - somehow keeps hydrogen ions close to the outer surface of the CM such that they cannot spontaneously combine with OH- to form H2O 70b hybridization 71a the process in which single-stranded, denatured DNA can form hybrid ds molecules with other ss DNA or RNA by complementary or almost complementary base pairing 71b Importance of Metabolome Analysis 72a important in study of biochemistry such as monitoring the levels of secondary metabolites (in plants or microbes) or the production of metabolites by humans in response to different conditions 72b inducer 73a substance that promotes enzyme synthesis (ex: lactose) 73b induction 74a the opposite of repression; transcription is UNBLOCKED in response to a signal; usually affects catabolic enzymes 74b insertion sequences 75a -simple transposable elements whose genes encode only transposition -found in organisms undergoing rapid evolutionary change 75b interactome 76a complete set of interactions among macromolecules within a cell; often so complex when it comes to mapping the interactions that it is more efficient to use a focused network such as the mobility protein network of Campylobacter jejuni 76b Interesting fact: the compatible solute of


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