Microbiology Exam #1

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Microbiology Exam #1
2013-09-23 14:52:59
microbiology chapter test

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  1. microbe general definition
    a living organism that requires a microscope to be seen
  2. microbial cells range from
    mm to .2 micrometer
  3. compared to microbes, viruses may be 10 times smaller
  4. 2 characteristics of a microbe
    • consists of a single cell
    • contains in its genome the capacity to reproduce its own kind
  5. 3 exceptions to microbes
    • super sized microbial cells
    • microbial communities
    • living
  6. super sized microbial cells
    usually you need a microscope to see microbes but sometimes they are large enough for the naked eye to see
  7. microbial communities
    multicellular assemblages
  8. living microbial cells
    viruses,viroids, and prions are not able to be seen with the naked eye but are considered microbial cells
  9. what is a virus
    a non-cellular particle containing a genome that can replicate only inside a cell
  10. out of the 3 domains, what do microbes associate with more
    • bacteria
    • archae
  11. microbes dont get associated with plants or animals
  12. genome
    organisms total genetic content
  13. have the greatest diveristy of genomes
  14. 2 importances as to why its good that microbes have the greatest diversity of genomes
    • importance for understanding evolution
    • comparative genomics shows core genes
  15. 2 ways microbes affect food +/-
    • preserves food
    • destroy crops
  16. 3 microbial diseases that changed history
    • black plague
    • small pox
    • HIV/AIDS
  17. built the first compound microscope
    robert Hooke
  18. first manuscript that illustrated objects under the microscope
  19. coined the term cell
  20. built single lens magnifiers
    antoni van leeuwenhoek
  21. first to observe single cell microbes
  22. showed maggots in decaying meat were the offspring of flies
  23. showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes
  24. discovered the microbial basis of fermentation
  25. devised swan neck flasks
  26. showed that after boiling the contents remained free of microbes despite access to air
  27. founder of the scientific method of microbiology
  28. devloped pure culture techniques and the petri dish and agar
  29. kochs 4 postulate
    • microbe is found in all cases of the disease but is absent from healthy individuals
    • microbe is isolated from the diseased host and grown in a pure culture
    • when the microbe is introduced into a healthy host, the same disease occurs
    • same strain of microbe is obtained from the newly diseased host
  30. introduced the practice of small pox inoculation to europe in 1717
    mary montagu
  31. deliberately infected patients with matter from cowpox lesions
  32. practice of cowpox inoculation was called
  33. developed the first vaccines based on attenuated strains
  34. 2 vaccines pasteur developed
    • fowl cholera
    • rabies
  35. immunization
    stimulation of an immune response by deliberate inoculation with an attenuated pathogen
  36. discovered penecillium
  37. purified penecillium (2)
    • florey
    • chain
  38. the first commercial antibiotic to save human lives
  39. endosymbiosis
    eukaryotic organelles (mito/chloro) evolved from the endosymbiosis from prokaryotic cells engulfed by proto-eukaryotes
  40. studying recently discovered prokaryotes in hot springs
  41. analysis of the 16S rRNA that woese did was that these prokaryotes were a distinct form of life
  42. the prokaryotes found in the hot springs were founded to be
  43. his discovery that replaced the five kingdoms with 3 domains
  44. led to the recombinant DNA
    restriction endonucleases
  45. A heat stable DNA polymerase was used for
    amplifying DNA via polymerase chain reaction
  46. disproved spontaneous generation
  47. microbes are organisms that include these 6
    • bacteria
    • archaea
    • fungi
    • algae
    • protists
    • viruses
  48. microbes perform unique roles in geochemical cycling
  49. advances in microscopy and biochem revealed that the structure and function of the various cell components
  50. genome
    total genetic info contained in an organisms chromosomal DNA
  51. the first genomes to be sequenced were those of viruses. Whose complete DNA sequence was determined was that of a
  52. bacteriophage
    a virus that infects bacteria
  53. built the first compound microscope
  54. first individual to observe single celled microbes
  55. published a book which illustrated what was seen in the microscope
  56. believed that heat killed microbes when we saw that his teeth were free of microbes after drinking hot coffee
  57. his experiment about keeping meat in a sealed container caused him to argue against spontaneous generation
  58. to disprove spon gen he showed that a sealed flask of meat brother sterilized by boiling failed to grow microbes
  59. discovered cell fission
  60. discovered the fundamental chemical rpoperty of chirality
  61. founded that nutrient substances containing both mirror forms only had 1 form that was fundamental property for life
  62. fermentation
    process by which microbes gain energy by converting sugars into alcohol
  63. device pasteur came up with
    unsealed flask with a long bent swan neck that admitted air but kept the boiled contents free of microbes
  64. autoclave
    a standard method for the sterilization of materials required for the controlled study of microbes
  65. showed that repeated cycles of heat was necessary to eliminate spores formed by bacteria
  66. used medical statistics demonstrate the significance of mortality due to diseases
  67. theory that many diseases are caused by microbes
    germ theory of disease
  68. first to determine that a specific microbe causes specific disease
  69. koch demonstrated an important principle of epidemiology
    chain of infection
  70. a culture grown from a single parental cell
    pure culture
  71. due to this surgeon fully aseptic environments for surgery and treatments for wounds
  72. made his staff wash their hands with an antiseptic agent after dissecting cadavers
  73. founded penicillin
  74. molecule that killed microbes alone and leaving their host unharmed
  75. (2)purified penicillin and made it the first commercial antibiotic to save lives
    • florey
    • chain
  76. chemolithotrophs
    organisms that feed solely on inorganic minerals
  77. use of selective growth media that supports certain classes of microbial metabolism while excluding others
    enrichment culture
  78. nitrogen fixation
    bacteria and archaea fix nitrogen by reducing it to ammonia
  79. first developed a system of enrichment culture
  80. polyphyletic
    multiple ancestry of living species
  81. recognized that microbes constitute a form of life distinct from animals and plants
  82. transformation
    dead bacteria could carry genetic info into living cells transforming harmless bacteria into harmful bacteria
  83. DNA sequencing
    the reading of the sequence of DNA base pairs
  84. restriction endonucleases led to recombinant DNA
  85. restriction endocleases
    bactera made, enzymes that cut DNA at positions determined by specific short base sequences
  86. how to make recombinant DNA
    by gene cloning, made it possible to transfer genes between the genomes of virtually all types of organisms
  87. gene regulation discovered in bacteria provided models for animals and plants
  88. recombinant DNA
    combining the DNA from more than one species
  89. 3 ways of cell transports
    • pass diffusion
    • transporters
    • pumps
  90. what 3 characters are need to go through passive diffusion
    • small
    • membrane permeant
    • weak acid and bases
  91. transporters pass material into/out of the cell
  92. pumps use energy such as ATP to
    move materials against their gradient
  93. Generation of proton motive force
    proton pumps push protons out of cell
  94. what 2 things work against the proton motive force
    • osmotic and electrical forces
    • (tries to push protons back into cell)
  95. PMF is used to create ATP
    ATP synthase uses PMF for energy
  96. cell walls peptides can form cross bridges connecting the parallel glycan strands
  97. the bacterial wall is made up of these 2 long polymers
    2 disaccharides called n-acetylglucosamine and N-acetylmuramic acid, bound to a peptide of 4-6 amino acids
  98. 4 characters of a gram positive envelope
    • capsule
    • s layer
    • thick cell wall
    • plasma membrane
  99. Capsule
    s layer
    gram positive is made up of
    • polysac
    • proteins
  100. 5 characters of gram negative envelope
    • capsule
    • outer membrane
    • thin cell wall
    • thick periplasm
    • plasma membrane
  101. the outer mem of the outer leaflet only of a gram negative envelope is made of
  102. the thin cell wall of a gram negative envelop is made up of
    amino acid crosslinks in peptido
  103. 3 bacterial cytoskeleton
    • MreB protein
    • FtsZ
    • CreS
  104. cytoskeleton forms a coil inside rod shaped cells
    MreB protein
  105. Forms a z ring essential for cell separation
  106. curves inner side of crescent shaped bacteria
  107. 3 characters of bacterial nucleioid
    • single look of double strand DNA
    • attached to cell envelop
    • replicates once for each cell division
  108. single loop of double stranded DNA from a bacterial nucleoid is compacted via supercoling
  109. gene expression in bacterial cells processes occur simultaneously
  110. 3 steps of cell division of bacteria
    • cell elongates as it grows
    • DNA replicates to make 2 X
    • cell undergoes separation
  111. as the cell elongates as it grows in bacteria cell division it adds a new wall at cell equator
  112. when DNA replicates in bacteria division
    DNA replicates bidirectionally and begins next rep before cell divides
  113. carboxysomes fix carbon and use energy to make sugar
  114. phycobillisome proteins collect light energy in cyanobacteria
  115. 4 storage granules of bacteria cells
    • glycogen (sugar for E)
    • PHB (fatty acid polymer for E)
    • polyphosphate (store material)
    • sulfur for disposal
  116. 2 characters of gas vesicles
    • gas filled structures made of proteins
    • confers buoyancy
  117. reason to orient the cell along magnetic field line for magnetotaxis
    help find correct oxy concentration
  118. 4 characters for cell attachment
    • fimbriae and pili attach cells to surfaces
    • stalks attach cells to surfaces
    • sex pilus is similar to type IV secretion systems
    • essential for bacterial pathogenicity
  119. pilin
    thin filaments of protein
  120. stalks that are attached to cells surfaces are
    an extension of cell cytoplasm
  121. 5 reason bacteria build pili
    • surface motility
    • adhesion to biotic/abiotic surfaces
    • aggregation to form microcolony
    • transfer DNA to other cells
    • bacteriophage attachment
  122. flagella rotate to propel cell
    proton passage drives rotation CW or CCW
  123. peritrichous
    flagella all over the bacteria cell
  124. polar
    flagella at one end of bacteria cell
  125. lophotrichous
    multiple flagella at one end of bacterial cell
  126. attractants cause CCW rotation
    • flagella bundle
    • push cell forward
  127. repellents to cell cause CW rotation
    flagella fly apart together
  128. change of direction
  129. runs and tumbles cause random walk
    receptor detect attractant concentrations
  130. attractant concentration increases and prolongs run
    • random walk
    • net movement of bacteria toward attractants
  131. when bacteria divide by binary fission
    cell growth and DNA rep are coordinated
  132. these 2 are used for attachments
    • pili
    • stalk
  133. 2 uses of flagella
    • movement
    • chemotaxis
  134. 3 fundamental traits of prokaryotes
    • thick outer envelop
    • compact genome
    • tightly coordinated cell function
  135. function of the outer envelop of the bacterial cell
    protects cell from environmental stress and predators
  136. have very little noncoding DNA
  137. the coordination of the prokary cell enables high reproductive rate
  138. the cytoplasm is contained by the
    cell membrane
  139. the cell membrane is composed of
    phospholipids, hydrophobic proteins, and other molecules
  140. the cell wall of a bacteria extends within the
  141. an aqueous layer that contains proteins such as sugar transporters
  142. what 2 things lie on the outer membrane of the cell wall
    • phospholipids
    • lipopolysaccharides
  143. a class of lipids attached to long polysaccharides
  144. the  bacterial cell wall and outer membrane constitute the
  145. the lipopolysaccharides and other polysac can generate a thick
  146. cell wall of protists is called
  147. the pellicle of the fungus consists of
    membranous layers reinforced by protein microtubules
  148. 4 chemical components all cells share
    • water
    • essential ions
    • small organic molecules
    • macromolecules
  149. a major class of organic cations
  150. molecules with multiple amine groups that are
    + charged and neutral PH
  151. total proteins encoded by a genome capable of expression in the cell
  152. created the first protein catalog of E.coli using 2D gels
  153. are protected by a thick cell envelope
    prokaryotic cells
  154. this maximizes reproductive potential with minimal resources
    compact genome
  155. the bacterial cell gene expression occurs all at once, for example as the mRNA is being made ribosomes are at the same time making proteins
  156. 3 ways to study functions of ribosomes by isolation and analysis of their parts
    • subcellular fractionation
    • structural analysis
    • genetic analysis
  157. enables isolation of cell parts so we can study their form and function
    subcellular fractionation
  158. by x-ray crystallography and related methods reveals the form of cell components
    structural analysis
  159. dissects the function of cell components based on construction of mutant cells with altered functions
    genetic analysis
  160. 4 ways to isolate parts of the cell
    • mild detergent lysis
    • freezing and thawing
    • sonication
    • enzymes
  161. general term for the contents of a broken cell
  162. the rate at which particles of a given size and shape travel to the bottom of the tube under centrifuge force
    sedimentation rate
  163. limitation of subcellular fractionation
    gives clues about the internal structure but provides little info about the processes
  164. crystallographic analysis applies only to isolated particles and under conditions in which its full function cannot be observed
  165. limitation of crystallography
    solve structures for proteins and nucleic acids capable of crystallization, not practical for flexible proteins or membrane soluble proteins
  166. shows which genes and proteins are responsible for functions of subcellular complexes
    genetic analysis
  167. 2 functions of the cell membrane
    • mediates transports between the cytoplasm and the external medium
    • carries many proteins with specific functions
  168. the phospholipid has a hydrophobic tail and a hydrophilic head
  169. phospholipid structure consists of these 3
  170. the 2 layers of phospholipids in the bilayer
  171. 3 functions of membrane proteins
    • structural support
    • detect environmental signals
    • secretion of viral factors and communication signals
  172. membrane proteins form secretion complexes to export toxins and cell signals across the envelope
  173. proteins embedded within the membrane must have a hydrophobic portion that is soluble within the membrane
  174. pressure on cell membrane resulting from osmosis
    osmotic pressure
  175. small uncharged molecules such as gas and water examples of diffusion
    passive diffusion
  176. membrane permeant weak acids: cross uncharged then bound/unbound to an open H+, this causes acid or alkai stress
    a high proton conc outside of cell will up the amnt of uncharge weak acid that can enter the cell, vice versa
  177. key substances in cellular metabolism are
    membrane permeant weak acids and bases
  178. protein enable transport that is highly selective and will only transport certain nutrients and ions under different environmental conditions
    transport proteins
  179. organisms that live in complex changing environments express numerous transporters
  180. the ion gradient (ratio of conc) across the cell membrane can store energy obtained from metabolizing food from photosynthesis
  181. hydrogen ion gradient plus the charge diff across the membrane form
    electrochemical potential
  182. proton potential (proton motive force) drives the membrane bound
    ATP synthase (provides most of the ATP for aerobic respiring cells)
  183. phosphoryl head groups carry a net charge of negative, thus they are called
  184. the negatively charged phosphatidate could contains various organic groups  such as glycerol to form phosphatidylglycerol
  185. some phospholipids can have positively charged heads such as phosphatidylethanolamine
  186. 2 examples of locations of + phosphoryl heads
    • membranes that interact with - DNA
    • trnasporter proteins that require interaction
  187. what are terpene derivatives and their function in the membranes
    planar molecules that stiffen and reinforce the membrane
  188. in eukaryotic membranes the terpene derivatives are
    sterols (cholesterol)
  189. bacteria's membranes are stiffened by pentacyclic hydrocarbon aka
  190. terpene derivative found in archael hydrocarbon chains are
  191. terpenoids are polmeric structures derived from
  192. in this structure to stiffen membranes, every 4th C extends a methyl branch
  193. the branches from the terpenoids strengthen the membrane by limiting movement of hydrocarbon chains
  194. ether linked lipids
  195. ester linked lipids
    bacteria and eukaryotes
  196. the terpenoids cyclize to form cyclopentane rings which stiffen the mebrane to a greater extent
  197. the cell membrane consists of phospholipid bilayers containing hydrophobic membrane proteins
  198. 3 examples of cell mem protein functions
    • transport
    • cell defense
    • cell communication
  199. the bacterial cell wall
  200. the cell wall 2 functions
    • helps to withstand turgid pressure due to osmosis
    • confers rigidity
  201. consists of a single interlinked molecule that encloses the entire cell
  202. a polymer of peptide linked chains of amino sugars
  203. peptidoglycan aka
  204. glycan chains are linked by peptide cross bridges
  205. the cross linked peptides of neighboring glycan strands form the cage of sacculus
  206. have a thick cell wall with multiple layers of peptidoglycan, interpenetrated by teichoic acids
    gram + bacteria
  207. have thin cell walls enclosed by an outer membrane
    gram - bacteria
  208. the peptidoglycan in gram + is reinforced by
    teichoic acids threaded through multiple layers
  209. teochoic acids can be made up of these 2
    • phosphodiester linked glycerol
    • ribitol w/amino acids linked to middle OH groups
  210. outside the cell wall of the gram + is often encased in
  211. an additional layer found in gram  + and as well as archae
  212. is a crystalline layer of thick subunits consisting of proteins or glycoproteins
  213. loss of trait occurs in th absence of selective pressure for genes encoding the trait
    reductive evolution
  214. the inward facing leaflet on the outer cell mem has a phospholipid composition similar to
    the inner cell membrane
  215. lipoproteins are found where
    outer membranes inward facing leaflet
  216. major lipoprotein
    murein lipoprotein
  217. the outwater facing leaflet on the outer mem consists of a special kind of phospholipid called
  218. endotoxin
    cell component that is harmless as long as pathogen is intact unlessreleased by a lysed cell
  219. in lipopolysaccharides the fatty acids are esterified to glucosamine
  220. an amino augar found in peptidoglycan and the outwater facing leaflet on the outer mem
  221. two glucosamine dimers each condense with 2 fatty acid chains which makes 4
  222. 1 of the glucosamines on the outward facing leaflet is attached to
    core polysaccharide
  223. sugar chain that extends outside the cell
    core polysaccharide
  224. the core polysaccharide extends to the
    o polysaccharides
  225. a chain with 200+ sugars
    o polysaccharide
  226. the outer membrane may contain unique proteins that are not found in the inner membrane vice versa
  227. outer membrane proteins of pathogens are important targets for vaccine development
  228. these permit the entry of nutrients such as sugars and peptides
  229. outer membranes contain a class of transporters called
  230. the outer membrane porins have a distinctive cylinder of beta cheets known as a beta barrel
  231. cells express different outer membrane porins under different environmental pressures
    ex in dilute environments, cells express porins of large pore size
  232. the region between the inner and outer membrane of gram - defines a seperate membrane bound compartment called
  233. this found in gram - contains specific enzymes and nutrient transporters for found within the cytoplasm
  234. eukaryotic microbes that dont have a cell wall possess a
    contractile vacuole
  235. function of contractile vacuole
    pump water out of the cell to avoid osmotic shock
  236. is highly porous but can prevent phagocytosis and phage infection
    s layer in bacteria
  237. the s layer in archaea function
    cell wall
  238. a capsule can be found in both gram +/-
  239. 2 function of gram - outer mem
    • regulates nutrient unptake
    • excludes toxins
  240. the envelope layers of this outer membrane include protein pores and transporters of various selectivity
    gram - outer mem
  241. important function of cell envelope in bacteria
    protect cells genome
  242. the DNA organized in loops in bacterial cells
  243. the domains of a bacterial cell connect back to a central point called
    origin of replication
  244. 3 in bacterial DNA replication
    • double helix unzips
    • replication begins outward in both directions
    • no resting phase, while cells replicate the DNA the two replicated origins may split again before even complete
  245. supercoiling (think of a phone cord) becoms compact
  246. mRNA strands dotted with ribosomes
  247. enzyme complexes that help fold the new peptide into its functional tertiary structure
  248. as translation begins the signal sequence binds to a
    signal recognition particle
  249. an RNA protein complex
  250. SRP complex function
    transfers the polypeptide ribosome mrna complex bearing the signal sequence to the secretory complex within the cell mem
  251. in prokaryotes its circular chromosome replicates at the origin but from both sides
  252. the replication fork is propagated by
  253. helicase function
    unwind the DNA helix ahead of replication and primase
  254. primase fucntion
    generate RNA primers
  255. the complex of DNA polymerase with its accessory components
    • replisome
    • (need two since bidirectional)
  256. the DNA termination site triggers growth of dividing partition of the envelope called
  257. the process by which septum occurs in cell division
  258. the process of septation generates most of the new cell envelop to enclose the expanding cytoplasm
  259. look at septation of bacteria
  260. normal division of bacteria doesnt always occur, assymetrical cell division gives rise to
  261. inert endospore is capable of remaining dormant but viable for years
  262. are microscopic membrane bound crystals of magnetic mineral magnetite
  263. magnetosomes generate a magnetic dipole moment along the length of the bacterium which causes it to swim along the magnetic orientation
  264. magnetosomes are anaerobces, and swims downward toward magnetic north
  265. the ability to attach a substrate
  266. the most common structures that bacteria use to attach a substrate is
  267. straight filaments of protein monomers are called
  268. serve to attach a male donor cell to a female recipient cell for the transfer of dna
    sex pili
  269. stalk's tip secretes an adhesion factor called