Micro Exam 2

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  1. increase in population of the microbe
    • microbial growth
    • NUMBER NOT SIZE
  2. study of inheritance and inheritable traits as expressed in an organism's genetic material
    genetics
  3. Bacteria have ____ but ___ is the only genetic martial that is passed on
    RNA

    DNA
  4. the entire genetic complement of an organism, includes its genes and nucleotide sequences
    genome
  5. True/False Virus can have RNA or DNA and they can pass either on to their offspring
    TRUE
  6. a rare event that is almost always deleterious and results in a change in the nucleotide base sequence of a genome
    mutation
  7. true/false: mutations provide diversification and without them life would have stopped however they can cause problems in the individuals
    true
  8. True/False: mutations rarely leads to a protein that improves ability of organism to survive
    TRUE
  9. Bacteria reproduces to make a new organism asexually (cell turn over). Bacterial sex is not involved in _____ BUT IS INVOLVED in ____ the DNA (horizontal gene transfer)
    reproduction 

    diversifying
  10. ____ phage caries random DNA segments from donor to recipient is referred to as:
    transduction

    generalized transduction
  11. transduction where only certain donor DNA sequences are transferred
    specialized transduction
  12. True/False: humans engage in transduction
    FALSE
  13. steps of transduction:

    1. bacteriophage injects _____
    2. phage ____ degrade host DNA
    3. Cell synthesizes new _____ that incorporate phage DNA and mistakenly, some ____ DNA and they break out of the cell
    4. Transducing phage injects ____ DNA
    • 1. DNA
    • 2. enzymes
    • 3. phages, host
    • 4. donor
  14. in bacterial conjugation which cell creates the pilus?
    the donor cell
  15. DNA in bacteria conjugation is known as a
    plasmid
  16. True/False: the plasmid provides genes for essential nutrients and enzymes in the cell
    FALSE
  17. True/ False: a plasmid can give a cell all kinds of additional genes and could make a difference
    TRUE
  18. Bacterial Conjugation Steps:

    1. donor cell attaches tot a recipient cell with its _____
    2. pilus ____________
    3. one strange of _____ DNA transfers over to the recipient
    4. the recipient synthesizes a ______ strand and the donor synthesizes a ______ strand, restoring its complete plasmid
    • 1. pilus
    • 2. draws the cells together 
    • 3. plasmid
    • 4. complementary, complementary
  19. The piece of plasmid DNA is independent of the host chromosome—has an____ ____ _____  and a degree of _____ because it can replicate on its own
    • origin of replication
    • autonomy
  20. segments of DNA that move from one location to another in the same or different molecule
    transposons
  21. True/False: transposons result in a kind of frameshift insertion
    True
  22. True/False: humans have transposons in their genes
    TRUE
  23. True/False: transposons can jump from one place to another on a DNA molecule and may replicate while moving resulting in a greater number of transposons in the cell
    True
  24. True/False: transposons can jump to plasmids and be transferred to another cell
    True
  25. True/False: in transduction, the bacteria and phage contribute sequences
    FALSE

    ONLY looking at BACTERIAL sequences, the phage doesn't contributed any sequence
  26. presence of the phage establishing lysogeny and contributing a phage gene
    Lysogenic conversion
  27. True/False: If a virus infects a bacteria that virus can cause human disease directly
    FALSE

    • it cannot cause human disease 
    • it wont effect us

    can cause problems indirectly but not directly
  28. donor cell contributes part of genome to recipient cell
    Horizontal Gene Transfer
  29. What are the three types of horizontal gene transfer
    • Transformation
    • Transduction
    • Bacterial Conjugation (associated to pilli)
  30. result of microbial growth on a plate is _____ _____
    discrete colony
  31. bacterial production is ______ (asexual)
    uni-parental

    starts with a single cell--it is asexual
  32. True/False: organisms have enzymes to build and breakdown molecules that they need and it is encoded in their DNA
    TRUE
  33. most common nutrients contain necessary elements such as (4):
    • carbon
    • oxygen
    • nitrogen
    • hydrogen
  34. True/False: Nutrition goes beyond energy for bacteria just like it does for us
    TRUE

    example: cant survive on sugar alone, does provide energy but doesn’t have necessary nutrients 
  35. microbes obtain nutrients from a _____  of sources
    VARIETY
  36. two groups of organisms based on source of carbon
    autotrophs

    heretrophs
  37. self-feeding and make their own sources of carbon
    autotrophs
  38. True/False: every autotroph is photosynthetic
    FALSE
  39. get their source of carbon from other sources (not themselves)
    heterotrophs
  40. two groups of organisms based on source of energy
    • chemotrophs
    • phototrophs
  41. organisms that get their source of energy from chemicals
    chemotrophs
  42. get their source of energy from light
    phototrophs
  43. ___ and ____ complementary of each other

    ____ create sugar and give off oxygen
    ______ (humans) take in oxygen and eat the sugar and give off CO2 for the autos
    heterotrophs, autotrophs

    • auto
    • hetero
  44. which chemoheterotrophs participate in aerobic respiration (4)
    • most animals
    • fungi
    • protozoa
    • many bacteria
  45. which chemoheterotrophs participate in anaerobic respiration (4)
    • some animals
    • protozoa
    • bacteria
    • archaea
  46. which chemoheterotrophs participate in fermentation
    • some bacteria
    • yeasts
    • archaea
  47. oxygen is essential for _____ _____, but oxygen is deadly for _____ _____
    obligate aerobes

    obligate anaerobes
  48. Parts of the body with rich anaerobic normal microflora (3)
    • mouth
    • GI tract
    • female genital tract
  49. True/False: We are obligate aerobes but some cells in our body are anaerobic
    TRUE

    RBC—carry it but don’t use it, are sensitive to O2 but are not equipped to use it
  50. Why are free radicals/ROS very dangerous to obligate anaerobes but not as much to facultative anaerobes?
    These are VERY dangerous to obligate anaerobes bc they cannot live with oxygen but are not very dangerous to falcultative anaerobes bc they can live with oxygen if need be
  51. True/False: every part of the human body is saturated with oxygen
    FALSE

    We have anaerobic bacteria living in us and they need anaerobic conditions
  52. What are the two environments that anaerobic bacteria can live in in our bodies
    May be living in an environment present with aerobic bacteria (they are taking in all of the oxygen)

    May be living in an environment where the O2 is hidden by something or by a fluid (oxygen has LOW solubility in fluid—must be carried in the RBCs)
  53. True/False: there is a lot of indigenous anaerobic flora in the human body
    TRUE
  54. Anaerobic bacteria in the human mouth out number the aerobic bacteria ___:___
    10: 1
  55. True/False: Tooth surfaces also have more anaerobic bacteria
    TRUE
  56. In the gums, anaerobic bacteria out number the aerobes _____:____
    1000: 1
  57. what are the four toxic forms of oxygen and which is the most dangerous?
    • singlet oxygen
    • superoxide radicals
    • peroxide anion
    • hydroxyl radical (MOST dangerous)
  58. do anaerobes possess superoxide dismutase?
    NO! because it catalyzes a reaction that produces oxygen and it will kill them
  59. do anaerobes possess catalase?
    NO! because it catalyzes a reaction that produces oxygen and it will kill them
  60. ____ ___ is molecular oxygen with electrons that have even boosted to a higher energy state. It is a very reactive oxidizing agent
    Singlet oxygen
  61. ____ ____ can be formed during the incomplete reduction of O2 during electron transport in aerobic organisms and during metabolism by anaerobes with the presence of oxygen.
    superoxide radical
  62. ____ ____ can detoxify superoxide radicals thus: 2O2- + 2H+ --> H2O2 + O2
    superoxide distmutase
  63. ___ ___ is a highly creative oxidant. IT is what makes hydrogen peroxide an antimicrobial agent.
    Peroxide anion
  64. ____ converts peroxide into water and oxygen (safe products)

    2H2O2--> 2H2O + O2
    catalase
  65. ______ breaks down hydrogen peroxide

    H2O2 + NADH + H+ --> 2H2O + NAD+
    peroxidase
  66. _____ ____ either lack both catalase and peroxidase or have a small amount of them
    obligate anaerobes
  67. _____ ____ is a product of ionizing radiation and the incomplete reduction of H2O2 : H2O2  + O- + H+ --> H2O + OH
    hydroxyl radical

    MOST reactive of the 4 toxic forms of oxygen
  68. in the catalase test what will indicate a positive presences of catalase?
    bubbles in the solution--since catalase breaks down H2O2 and produces water and O2 the O2 gas will form bubbles so you know catalase is working
  69. The catalase test is very ____
    fast
  70. 5 types of bacteria with varying oxygen requirements
    • Aerobes
    • Anaerobes
    • Facultative Anaerobes 
    • Aerotolerant Anaerobes 
    • Microaerophiles--live in about 2-10% oxygen
  71. where are obligate aerobes in a test tube?
    towards the top
  72. where are obligate anaerobes in a test tube?
    at the bottom
  73. where are facultative anaerobes in a test tube?
    throughout but mostly towards the top
  74. where are aerotolerant anaerobes in a test tube?
    pretty even throughout but kinda more towards the top
  75. where are microaerophiles in a test tube?
    they are scrunched in the middle
  76. for the test tube experiment you cannot use a normal broth, you need to add what?
    a reducing agent!

    Commonly used: thioglycolate
  77. True/False: aerotolerant anaerobes are strictly anaerobic but oxygen does NOT kill them
    TRUE
  78. Facultative anaerobes can go either way but you find more at the top (near more oxygen)—why?
    They can use oxygen to grow faster—aerobic metabolism is much more efficient than anaerobic
  79. anabolism often ceases due to insufficient _____
    nitrogen
  80. what would be the rate limiting factor in anabolism if you don't have N?
    protein! you need protein for life
  81. nitrogen is acquired from ____ and _____ nutrients
    organic and inorganic
  82. ____ ____ by certain bacteria is essential to life on Earth
    nitrogen fixation
  83. Molecules with Nitrogen (3)
    • amino acids
    • nucleotides
    • Hb
  84. If you don’t have N what would be causing more of a problem earlier—Nucleotides or proteins?
    Nucleotides because they CODE for the amino acids
  85. the effect of temperature on proteins and can be:
    mild

    it isn't all or nothing
  86. effect of temperature on lipid-containing membranes of cells and organelles:

    if too low:
    if too high:
    membranes become rigid and fragile

    membranes become too fluid
  87. True/False: in thermophiles and hypothermophiles, proteins are not denatured
    TRUE

    they have a variety of different mechanism that allows them to survive in High T environments
  88. thermophiles and hypothermophiles are mostly ___ not ____ but some can be
    archaea

    bacteria
  89. ______ is a part of growth rate but not the only factor
    denaturation
  90. True/False: it doesn't take a lot of temp change to kill the bacteria
    True

    thats how fever works
  91. How do human bacteria growth on plates in the following temperatures: 

    22*C--room T

    30*C

    37*C—body temperature
    • 22*C-- don't grow well
    • 30*C--grow a little bit better, getting closer to body T
    • 37*C--grow the best at body temperature (this is optimal)
  92. bacteria that have peak growth around 10*C
    psychrophiles
  93. bacteria that have peak growth around 35*C
    mesophiles (found in our body)
  94. bacteria that have peak growth around 65*C
    thermophiles
  95. bacteria that have peak growth around 90*C
    hyperthermophiles
  96. How do acidity changes affect  bacterial proteins and DNA?
    the H+ and OH- ratios interfere with hydrogen bonding and in proteins and DNA they have this bonding
  97. grow best in a narrow range around neutral pH
    neutrophiles
  98. grow best in acidic habitats (found in yogurt and live in our digestive tracts)
    acidophiles
  99. live and grow best in alkaline soils and water
    alkalinophiles
  100. Microbes require ____ to dissolve enzymes and nutrients
    water
  101. most cells die in the absence of water-- but some cells have walls that retain water such as:
    • endospores
    • cysts (an aspiring endospore and found in many organisms)
  102. two physical effects of water
    • osmotic pressure
    • hydrostatic pressure
  103. the pressure exerted on a  semipermeable membrane by a solution containing solutes that cannot freely cross membrane
    osmotic pressure
  104. complex relationships among numerous microorgaisms (could be members of the same species or extend to different species)
    Biofilms
  105. adering cells to one another, attaching to a substrate (bottom layer of something), and sequestering nutrients allow bacteria in a biofilm to
    develop an extracellular matrix
  106. sensing the population around them--how many other bacteria are present
    quorum sensing
  107. a critical number of individuals that need to be present
    quorum
  108. why are microorganisms more harmful (successful) as part of a biofilm
    they develop partial multi-cellularity and are able to work in a team
  109. comes from feel matter and by collecting it from the environment and growing it you can get information on what type of bacteria is there in the are that you collected and the numbers
    Coliform Bacteria
  110. clinical specimens come from
    a person
  111. environmental specimens come from
    the environment
  112. act of cultivating microorganisms or the microorganisms that are cultivated
    culture
  113. a culture with no strangers, what you are culturing is a specific bacteria and nothing else
    axenic culture
  114. what would it be good to culture a bacteria that is found in an HIV patient
    It would be a good idea to culture a bacteria that is found in an HIV patient because they are so immunocompromised that other things can grow that may not normally grow
  115. to introduce the bacteria to the medium and watch it grow
    innoculate
  116. cultures composed of cells arising from a single progenitor
    pure cultures
  117. what is a progenitor and how is it termed?
    the parent that produces something (the progeny)

    it is termed a CFU
  118. what is CFU used to determine?
    if something is alive

    if it can form a colony, you assume it is dividing so it is alive
  119. How can you check if a CFU is actually alive?
    transfer the bacteria and it if grows it is alive
  120. Why are visual or bacterial mass techniques to measure number of bacterial inaccurate
    That is not a very accurate way to measure because some bacteria can be dead—may not look a whole lot different (after a while they will but freshly dead they won't) and freshly dead bacteria will still weight as much as much
  121. why is it a good idea to have a flame when you are plating (2)
    Easy to pass the loop through it to sterilize it if you need to

    The hot air from the flame is rising and it helps minimize things from falling on your plate—less likely for air to fall and microbes to fall with the air (can also do it under a hood—will do the same effect)
  122. ___ technique prevents contamination of sterile substances or objects
    aseptic (sterile)
  123. two common isolation techniques
    • streak plates
    • pour plates
  124. How do you execute the streak-plate method of isolation?
    You want to be able to dilute each time

    Inoculate one—sterilize loop—streak some of one and make two—sterilize—streak some of three and make four
  125. why do you want to make a dilute colony when doing the streak plate method
    Want to make it more dilute so you can look at an individual isolate colony
  126. Why is not having nutrients in agar a good thing?
    by not having nutrients it allows you to add what you need to add

    if it did you would not know what nutrients are in it and it would be confusing to see what nutrients the bacteria needs
  127. T/F: all media has agar or another gelling agent to it
    False: not every media has agar in it– some media are liquid broths—in the pic above the test tubes have liquid broth and things are still growing!– add agar after
  128. Why don’t you fill the container completely up of broth (1 L of broth for a 4 L flask)
    The bacteria need oxygen—the 3 L of empty space is full of air for the bacteria
  129. what is serial dilution (pour plate method of isolation)
    you start with an initial sample and then add 1 mL of initial sample to 9mL of broth and then add 1ml of that to another 9mL of broth 


    Add 1 mL of the current solution to a petri dish and add 9 mL of warm agar and mix gently

    Take current 10 mL broth and take 1 mL of this and add to another 9 mL broth and then add 1 mL to another petri dish and add warm agar
  130. why have the majority of prokaryotes have not been grown in culture medium?
    we haven't gotten around to it or they can't be grown?

    why?--we don't know what they need (nutritional requirements) and what they can't tolerate
  131. medium where you know exactly what you are adding to the agar and simply follow the protocol
    Defined media (aka minimal media)
  132. what do you use defined media for?
    fastidious organisms (requiring very specific things)
  133. a media that we don't know exactly what is in it

    example:
    complex media 

    example: ground up yeast, beed or hydrolyzed proteins
  134. when would you use a complex media?
    when you want to grow something and you don't care what the nutritional requirements are and you just want to grow the bacteria and want it to work
  135. environment that will select for/against certain species of bacteria and that uses a marker to select

    example:
    selective media 

    example: add antibiotic to media to see what is resistant
  136. a medium where anything can grow there (not selective) but that is something that will differentiate what you are looking for
    Differential Media
  137. add a reducing factor or heat up the medium before using this type of media
    anaerobic media

    will cause the gaseous O2 to leave
  138. use this media when you don't want the bacteria to grow, you just want everything to stay the same and stay alive (very minimal media)
    transport media

    want to say stable while transporting it--if there is growth you will get a distorted profile on the number of bacteria and the type (due to competition)
  139. if you can't culture a bacteria what do you do
    they isolate it and then they do PCR to amplify DNA and then try to read from DNA what it might be
  140. If you cant grow a bacteria in culture media there is another way to grow it without using any culture, how?
    You can grow it in an animal that the bacteria infects
  141. slant in a tube shows evidence of what?
    growth
  142. Durham tube is used for what?
    to trap gas which indicates production of gas and growth (or fermentation)
  143. the GasPak is used for what?
    to create an anaerobic system and you are trying to remove the oxygen from the system
  144. two special techniques developed for culturing microorganisms
    animal and cell culture

    low-oxygen culture
  145. in a candle jar what bacteria are you trying to an environment for?
    capnophiles (CO2 loving)
  146. what is a way to preserve cultures for a short period of time
    refrigeration
  147. temptures:

    Room T:
    Body T:
    Refrigerator:
    Room T: low to mid 20s (22-25*C)

    Body T: 37*C

    Refrigerator: 4*C (40*F)
  148. preservation method that stores culture for years but must have certain chemicals in the dish before you do this
    deep-freezing
  149. what chemicals need to be added before deep-freezing
    glycerol is often used (this prevents it being frozen solid and it will be like a slurry)
  150. a way of preserving bacteria that is known as freeze drying and stores things for decades
    lyophilization
  151. what is a problem with freezing and defrosting?
    ice crystals can mess up the viability of the cells
  152. True/False: bacteria undergo nuclear fission/fusion
    FALSE

    can't talk about this with bacteria because they have NO nucleus
  153. fusion turns ____ bacteria into ____
    • 2
    • 1
  154. fission turns ___ bacteria into ____
    • 1
    • 2
  155. True/False: bacteria undergo mitosis
    FALSE 

    Don’t talk about mitosis with bacteria bc it is a part of the cell cycle and bacterial do NOT have a cell cycle
  156. what is the difference between logarithmic ad arithmetic growth
    logarithmic is multiplying by 2--doubling

    arithmetic--adding 2
  157. 2^10=
    2^20=
    2^30=
    2^40=
    • 2^10= ~ 1000
    • 2^20= ~1 million
    • 2^30= ~ 1 billion
    • 2^40= ~1 trillion
  158. time required for a bacterial cell to grow and divide and is dependent on chemical and physical conditions
    generation time
  159. what are the two chemical and physical conditions in which generation time is dependet
    biochemical

    genetics of the bacteria
  160. 5 direct methods for measuring microbial reproduction
    • serial dilution and viable plate counts
    • membrane filtration
    • most probably number
    • microscopic counts
    • electron encounters
  161. indirect methods of microbial growth (3)
    metabolic activity--creation of CO2 or utilization of O2

    dry weight--dry bacteria on a  filter

    turbidity--cloudiness=growth of bacteria
  162. what can be used to quantify the amount of bacteria based on turbidity?
    spectrophotometer
  163. True/False: the numbers that come from a spectrophotometer are the number of bacteria present
    FALSE!


    the numbers themselves don't mean anything unless you can compare it to other empirical results
  164. LOOK AT THE DIRECT METHODS OF MEASURING BACTERIA IN NOTES
    DONE
  165. genetic methods of measuring microbial growth include
    isolating DNA sequence of unculturable prokaryotes and use to estimate the number of these microbes
  166. phase where bacteria is synthesizing what it needs for reproduction (ribosomes, nucleic acid, enzymes, ATP)

    Very little to no growth
    lag phase
  167. where will the lag phase be longer: nutrient rich media or a nutrient poor media
    nutrient poor media because it needs to synthesize more things itself--in a nutrient rich media the things they need are in the media
  168. phase where there is exponential growth in numbers (NOT SIZE)
    log phase
  169. phase where bacteria stop growth and die
    stationary phase
  170. why do bacteria die during the stationary phase (2)
    lack of resources (space, oxygen, nutrients)

    waste build up from dying bacteria (more bacteria, more waste)--includes CO2 (unless they are capnophiles) and acidity--when bacteria die both of these seep from the bacterial carcass
  171. what is a way to prevent death in the stationary phase?
    use a chemostat--it will take away the waste and provide fresh media (nutrients)
  172. how to some bacteria get out of dying in the stationary phase (2)
    they form spores 

    they produce antibiotics and can fend themselves against other bacteria and out survive
  173. why is the stationary phase flatjQuery110106855092255864292_1509366932754
    the death rate is balancing the growth rate so no net growth or death--it is flat
  174. phase where the number of bacteria decline
    death (decline) phase
  175. True/False: the death phase is exponential
    TRUE
  176. two indicators of growth in a flask (physical)
    turbidity

    foul smell
  177. true/false: after bacteria growth a lot bacteria will be dead so you need to filter them out
    TRUE

    • how?
    • with a centrifuge or a filter
  178. what is the chemical that is needed by organisms and is found in ATP, DNA and RNA
    phosphorus
  179. a chemical that is required that is found in cysteine, methionine, and di-sulfide bonds
    sulfur
  180. True/False: We require a tiny amount of trace elements—too many can be toxic
    True!!

    we need some, but too much are very toxic to us
  181. necessary organic chemicals that cannot be synthesized by certain organisms
    growth factors
  182. True/False: humans get their growth factors from the environment
    FALSE

    we do not need them from the environment
  183. True/False: in most bacteria, growth factors must come from the environment
    TRUE
  184. what is an example of a bacteria that doesn't require growth factors
    E. Coli
  185. what is an example of a bacteria synthesizing a vitamin growth factor
    synthesis of folic acid from forming

    certain antibiotics: sulfadrugs in bacteria and methotrexate in humans inhibit this formation and therefore kill the bacteria (or cancerous cells)
  186. T/F: Some bacteria must import growth factors and others can make it but depends on the vitamin and the bacteria
    True
  187. what is an example of growth factors that humans can't make and must take in from the environment
    essential amino acids (essential in the diet)
  188. Growth factors depend on the bacteria we are looking at but could include (4)
    • amino acids
    • vitamins
    • purines
    • pyrimidines

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Author:
arikell
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Micro Exam 2
Updated:
2017-10-31 00:36:33
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