Biol 160 Exam 3

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Derek.Vargas1
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253412
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Biol 160 Exam 3
Updated:
2013-12-16 01:06:17
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Microbial Physiology
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Exam 3 / Final
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  1. Agar is used for
    separating DNA.
    False
  2. When you have only one plasmid to isolate, you need a new column for proper balance during
    centrifugation
    False
  3. After using a micropipette, it is desirable to set the volume to the maximum.
    True
  4. You use yellow tips for 10 ul micropipettes.
    True
  5. We used RNA primers for PCR amplification.
    False
  6. LB media contains 0.2% glucose.
    False
  7. In Biol 160 it is our normal procedure to take out enzyme and put on ice until use.
    False
  8. For the separation of large DNA fragments, we use a polyacrylamide gel.
    False
  9. For agarose gel electrophoresis, agarose will be dissolved in H2O.
    False
  10. A DNA size marker is composed of different sizes of circular DNA fragments.
    False
  11. Excess use of 6x dye is not recommended because it will affect DNA migration on an agarose gel
    False
  12. We normally do not wash or rinse the flask used for dissolving agarose.
    True
  13. When we made an agarose gel, we added EtBr to the gel.
    True
  14. For plasmid isolation, vigorous mixing is recommended after adding lysis solution
    False
  15. We use the same spin columns for both plasmid isolation and PCR clean-up.
    False
  16. Many bacteria can sense quorum and do so by direct cell-cell communication using pili.
    False
  17. If the genes for luminescence in a bacterial species are under the control of quorum sensing signal, luminescence is dependent upon cell density.
    True
  18. If the genes for luminescence in a bacterial species are under the control of quorum sensing signal, luminescence happens in high cell density above certain concentration.
    True
  19. Bacteria move toward higher concentration of chemical attractants by remembering the previous concentration over time.
    True
  20. Chemoreceptor proteins for chemoeffectors (attractants or repellants) are found in bacterial cell membrane.
    True
  21. The production of the same AI-2 by different types of bacteria in the same community is one way for the bacteria to engage in (            ) communication.
    Interspecies
  22. This term is for a community of microorganisms immobilized and living on a solid surface exposed to air or liquid. The obvious advantage would be a formation of food webs via the coordination of different types of microorganisms. What is this?
    Biofilm
  23. Chemoreceptor proteins for chemoeffectors are also called (        four words         ) (MCPs).
    Methyl-Accepting Chemotaxis Protein
  24. (           ) are unique among the known prokaryotes in that the cells aggregate and construct multicellular fruiting bodies.
    Myxobacteria
  25. When cultures of B. subtilis undergo nutritional limitation and enter the stationary phase, 10 to 20% of the cells ultimately develop (             ), which allows the uptake of external DNA.
    Competence
  26. Bacillus subtilis has evolved ways to adjust to stressful changes in the natural environement. One of these ways is to (     a         ) when faced with limiting supplies of a carbon or nitrogen source. The decision to (     a     ) is regulated by a phophorelay signal transduction system.
    Sporulate
  27. The normal flora are always beneficial.
    False
  28. Temperature can be a signal for virulence gene expression for pathogens.
    True
  29. Endotoxins are secreted in soluble form by live bacteria,
    False
  30. An enterotoxin is a protein toxin released by a microorganism in the intestine.
    True
  31. The enzymatic activity of Cholera toxin is ADP-ribosylation.
    True
  32. mRNA can sense environmental signals.
    True
  33. This bacterium, (               ), killed 75-200 million European people (one-third of the population at that time) in 1347 to 1353, known as the Black Death.
    Yersenia pestis
  34. This bacterium, (                    ) was first isolated by Italian anatomist, Filippo Pacini and also by Robert Koch as the cause of cholera.
    Vibrio cholerae
  35. This bacterium, (        ) is an opportunistic pathogen, meaning that can cause disease to an immunocompromised person, but not a healthy person. It typically infects lung, so it is a threat especially to a patient having Cystic fibrosis.
    Pseudomonas aeruginosa
  36. (            ) species cause gastroenteritis, enteric fever, and septicemia (blood infections)
    Salmonella
  37. (             ) species cause shigellosis and produces shiga toxin.
    Shigella
  38. This bacterium, (          ) is the causative agent of whooping cough. When you were very young, you probably got an immunization shot against this agent.
    Bordetella pertusis
  39. This bacterium, (           ) is the most common cause of staph infections, though it may exist as a commensal on human skin.
    Staphylococcous aureus
  40. (           ) is the causal agent of Crown Gall disease (the formation of tumors) in over 140 species of flowering plants. The bacterium has a mega-sized Ti plasmid (tumor-inducing plasmid).
    Agrobacterium tumefaciens
  41. When glucose is added to E. coli culture media, you will see a lot of glucose inside the bacterial cell.
    False
  42. In E. coli, glucose the best carbon source so if glucose is around, it represses the utilization of other carbon sources.
    True
  43. In E. coli, cAMP receptor protein is the transcriptional activator involved in catabolite repression. So, the effector (ligand) of the protein is glucose.
    False
  44. When E. coli cells see lactose (a decent carbon/energy source) outside, they always express lactose-utilization enzymes.
    False
  45. RNA polymerase prefers some DNA sites to bind to.
    True
  46. A transcription factor binds to target DNAs by recognizing a specific sequence.
    True
  47. Transcriptional activator helps RNA polymerase transcribe and repressor inhibits RNA polymerase from transcription.
    True
  48. In an operon, the binding site of a transcriptional activator always precedes the site for RNA polymerase (promoter).
    True
  49. In an operon, the binding site of a transcriptional repressor usually precedes the site for RNA polymerase (promoter).
    False
  50. Let’s say you know that the transcription of an operon strictly requires a transcriptional activator. Then the promoter for the operon is strong (& ideal).
    False
  51. How do you call DNA site to which a repressor binds?
    Operator Region
  52. Membrane protein cannot be a transcription factor.
    True
  53. Bacteria often use secondary messengers for environmental signals.
    True
  54. Obligatory anaerobes usually have oxygen-sensing transcriptional regulators such as FNR.
    False
  55. To kill host is the best interest for pathogenic bacteria.
    False
  56. Glucose is the best food for E. coli. So, glucose will repress utilization of any other carbohydrate in E. coli.
    True
  57. Many bacteria can sense quorum by direct cell-cell communication using pili.
    False
  58. There is no bacterium that can form multicellular fruiting bodies.
    False
  59. Several bacteria undergo sporulation when faced with nutrient excess.
    False
  60. In two-component systems, the sensor protein is always a transmembrane protein.
    True
  61. When bacteria encounter chemo-attractants (food), they tumble rather than swim.
    False
  62. mRNA can sense environmental signals.
    True
  63. Bacteria sense their environmental changes by recognizing signaling molecules and therefore there must be cellular components to bind to such signaling molecules.
    True
  64. All the environmental signaling molecules go into the cytoplasm in order to trigger appropriate adaptation mechanisms in bacteria.
    False
  65. Upon binding to signaling molecules, transcriptional regulators (or sensor proteins in two-component systems) undergo conformational changes (that is, there must be two protein forms in each case).
    True
  66. The regulation by altering protein’s activity is faster than that by changing the transcription level of the protein.
    True
  67. When glucose is NOT around, several glycolysis enzymes will be down-regulated through the alteration of the proteins’ activities.
    False
  68. The reactions catalyzed by regulatory enzymes are usually at a metabolic branch point.
    True
  69. Regulatory enzymes often catalyze reactions that are physiologically irreversible.
    True
  70. A positive allosteric effector would increase the Km of its protein.
    False
  71. For biosynthetic pathways, the end product is often a negative allosteric effector for a branch point enzyme. Such control is called end-product inhibition, or (      two words     ), by an end product.
    Feedback Inhibition
  72. The (            ) is the substrate concentration yielding 1/2Vmax.
    Km
  73. When the effector binds to the (          ) site (the effector site), the protein undergoes a conformational change, and this changes its kinetic constants.
    Allosteric
  74. Regulatory enzymes typically show (      ) kinetics, while non-regulated enzymes show (   ) kinetics.
    Sigmoidal, Michaelis-Menton
  75. There are three recognized patterns of feedback inhibition in biosynthetic pathways. What are those?
    Simple, Concertive, Cumulative
  76. When the binding of one substrate molecule increases the affinity of the enzyme for a second substrate molecule or increases the rate of formation of product from sites already occupied. This is called (          ) cooperativity.
    Positive
  77. Positive cooperativity makes enzyme catalysis very (         ) to small changes in substrate level concentrations.
    Sensitive
  78. Covalent modification of enzymes or proteins occurs by the reversible attachment of chemical groups such as (                 ) groups, (                      ) groups, (                     ) groups, (                 ) groups, and (                   ) groups.
    Acetyl, Phosphate, Methyl, Adenyl, Uridyl
  79. Sigma factors determine where RNA polymerase should bind.
    True
  80. The molecular weight of sigma32 is 32 kD.
    True
  81. Oxygen sensing proteins are all heme-containing proteins.
    False
  82. It is not the temperature per se that increases the activity and amount of sigma32, but rather the amount of (         ) protein.
    Denatured
  83. The toxic forms of oxygen include (                  two words       ), (      two words        ), and (              two words          ), which can damage molecules such as DNA, proteins, and lipids.
    Hydroxyl Radical, Superoxide Radical, Hydrogen Peroxide
  84. Reactive oxygen species can oxidatively damage guanine to form (                   ), which triggers GO system in bacteria.
    8-oxoguanine
  85. The most common (& bad) outcome of DNA damage by UV light is (two words)
    Thymine Dimers
  86. When E. coli cells are exposed to H2O2, OxyR is required to transcribe a set of genes for cellular defense and therefore will be activated. The active form of OxyR has an intramolecular (     two words    ) between two cysteine residues.
    Disulfide Bond
  87. List four functions of the E. coli heat-shock proteins:
    • 1. Folding newly synthesized proteins at all temperatures
    • 2. Export of proteins at all temperatures
    • 3. Refolding of misfolded polypeptides
    • 4. Proteolysis of improperly folded
    • proteins
  88. Acidic environment is easier for ATP generation via ATP synthase, so it is optimal for bacterial growth.
    False
  89. Bacteria maintain their internal pH and osmolarity by controlling water permeation (blocking/allowing water permeation) through the cell membrane.
    False
  90. Turgor pressure has nothing to do with bacterial cell growth and division.
    False
  91. In bacteria, turgor pressure is generally exerted across the outer membrane.
    False
  92. No bacterium can live in 5 M NaCl environment.
    False
  93. In the presence of high salt concentrations inside bacterial cells, ionic interactions (e.g. between amino acids in a protein) are weakened.
    True
  94. Bacteria can be found growing in habitats that vary in pH from 1 to 11. However, regardless of the external pH, the internal pH is usually maintained within 1 to 2 units of neutrality, which is necessary to maintain viability. Thus, bacteria maintain a pH gradient (DpH) across the (          two words        ).
    Cell membrane
  95. The regulation of intracellular pH is mostly a consequence of controlling the flow of protons across the cell membrane. On the other hand, for bulk proton to take place, the pumping must be done (        ). For example, when the cytoplasm becomes too basic, protons are brought in via exchange with outgoing (           ) or (          ).
    Electroneutrally, K+, Na+
  96. In alkaliphiles, the use of Na+/solute symporters is advantageous because solute transport is driven by the (      two words  ) rather than the (   two words      ), the latter being low because of the inverted (               ).
    Sodium Potential, Proton Potential,Δ pH
  97. In acidophiles, the maintenance of the large DpH requires an (   two words        ) at low pHout. In turn, this is due to an inward flux of (             ) greater than an outward flux of (              ).
    Inverted Membrane Potential, K+, Protons


  98. It looks like an acidophile has an advantage of having pre-existing proton potential, thus generating ATP through ATP synthase. But there is a problem without any compensatory mechanism. What is the problem?
    It costs energy to maintain the gradient


  99.  An alkaliphile should maintain the pH condition above. Then, what is the main challenge for these bacteria?
    Very little H+ outside the cell so it's difficult to make ATP
  100. Mechanosensitive channels exist in the cell membrane. (T/F)
    True
  101. Mechanosensitive channels are proteins. (T/F)
    True
  102. Mechanosensitive channels proteins should have strong interaction with lipid molecules. (T/F)
    True
  103. SoxR and OxyR are involved in transcriptional regulation by sensing superoxide and hydrogen peroxide, respectively. Then, their activity is DNA binding. (T/F)
    True
  104. What could be the main job(s) of heat shock proteins in bacteria (well, let's say E. coli) when temperature is higher than normal condition?
    Renature proteins or dispose of the denatured protein
  105. Role of rpoD
    Housekeeping sigma factor
  106. Role of rpoH
    Genes induced by heat shock
  107. Role of rpoS
    Genes for stationary phase
  108. Role of rpoE
    Genes for very high temperature
  109. Role of rpoN
    Genes for nitrogen metabolism
  110. Role of mutS
    Identify basepair mismatch problem
  111. Role of mutL
    Methylation
  112. Role of mutH
    Add nick to DNA
    • A. - ("simple")
    • B. -/- ("concerted")
    • C. -/- ("cumulative")
  113. If Km is high, this means: The enzyme has (              ) affinity to the substrate
    Low


  114. Which curve (A or B) shows more sensitivity in terms of enzyme activity in response to change in substrate level?
    A (sigmoidal curve)



  115. 1. Binding of + effector will (increase or decrease) Km of the enzyme.

    2.  Binding of - effector will (increase or decrease) Km of the enzyme.
    • 1. decrease Km
    • 2. increase Km
  116. All the molecules below can be environmental signaling molecules in bacteria.  Which one will penetrate cell membrane freely?
    a) NO3-
    b) K+
    c) Inorganic phosphate
    d) N-hexanoyl homoserine lactone
    N-hexanoyl homoserine lactone

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