Micro exam 2

  1. Ultimate goal is to maintain themselves and reproduce
    Anabolic Rxn
  2. Requires energy that is reserved.
  3. Are anabolic rxns endergonic or endogonic.
  4. are catabolic rxnx exogonic or endo?
  5. Change of G=
  6. What happoens when G is negative
    Exergonic and proceeds spontaneously
  7. What happens when G is postive
    endergonic and will not be spontaneous.
  8. A+B = C+D
  9. How are half rxns written?
    Thety are written as reductions. e- acceptor and electrons on the l;eft and potential e- donor on the right.
  10. the change of E is?
    The potential of the electron accptor couple minus the potentail of the e- donor couple.
  11. THis is the complete oxidation of glucose to CO2. Involves glycolysis, kreds cycle, and electric trans chain.
    Aerobic Resipration.
  12. How much ATP does Aerobic respiration yield.
  13. What is the terminal electron acceptor (TEA)
    Molecular O2
  14. This sis made mainly by oxidative phosphorylation
    ATP Some comes from substrate-level phosphorylation too.
  15. When looking at the redox couple chart where are the worst and best electron acceptors?
    Worst are at the top and best are at the bottom.
  16. when looking at the redox coupling chart where are the best electron donors and worst electron donorss?
    Thte best at the top and worst at the botom.
  17. A good way to remember the electron transport is H2 is a really good___ and O2 is a very good____
    E donor and E acceptor.
  18. Th is usually a complex oxidation of glucose to CO2m involves glycolysis, krebs, and alternative electron transport chain.
    Anaerobis respiration
  19. In anareboic repiration what is used to make ATP?
    NO3-, SO4- and FE+, and other inorganic compounds,
  20. Anaerobic respiration will only yield how much ATP?
  21. Incomplete oxidation of glucose. Some CO2 can be produced, but reduced products are also made. H2, organic acids, alcohol and/or other solvents
  22. How much ATP does fermentation yield?
    2 per glucose
  23. Used by strict aerobes, microaerophiles, and by most facultative anaerobes
    Aerobic Resp
  24. Used by some facultative anaerobes, some strict anaerobes. Mainly only performed by Bacteria and Archaea
    Anaerobi respiration
  25. May be used either by strict anaerobes or facultative anaerobes. Performed by some Bacteria, Archaea, fungi, and other Eukaryotes
  26. which of the three kinds of respiration will incompletly reduce the glucose?
  27. How is NADH reoxidized?
    Byb pyruvate or other products yeilding organic acids and solvents, COS and/or H2
  28. Which of the fermentation pathways produces GAS?
    Leuconostoc, e coli, enterobacter.
  29. Describe chlorophyll based phototrophy?
    Uses H2O and E donor, produces o2 and all are autotrophs. Anoxygenic ones will us H2F and the e donor and can uyse H2, Fe2 NO2 and organic compounds.
  30. What is an example of Rhodopsin based phototrophy.
    Involves a single protein and heterotropic.
  31. 1 circular chromosome Some may maintain multiple copies, but still always haploid Chromosome sizes vary from ~1 Mbp to ~10 Mbp (e.g. E. coli ~4.5 Mbp) High density of coding DNA (typically 85-90%)
    Bacteria and archea chromosome
  32. Typically multiple linear chromosomes; diploid Some microbial eukaryotes/fungi may be haploid for significant portions of their life cycle Typically much more genomic DNA (but not as high coding density)
  33. How does replication (and transcription, translation) machinery in Archaea compare to that in Bacteria and Eukaryotes?
    similar to Eukaryotes. Bacteria usually have a single origin of replication (ori), termination (ter) site Some Archaea have multiple origins of replication
  34. what is the usualt abbreviations for origin and terminus?
    ori and ter
  35. What is theta structure in reference to a partially replicated circular chromosome?
    Theta structure
  36. makes a double stranded break and passes one DNA strand through the gap, then closes the gap, unlinking chromosomes
    Topoisomerase IV
  37. How long does it take for e coli to replicate and double it generation?
    Rep takes 70 mins and doubling takes 20 mins
  38. How is the issue that ecoli has with replication fixed?
    The bacteria will start duplication on the outside an go towards the middle.
  39. What are the components of RNA Polymerase?
    Core is 2x alpha, beta, beta prime, and omega subunits. binds to a sigma factor to make a holoenzyme. The core does the transcription
  40. what are functional/structural differences between the holoenzyme and the core enzyme of RNA pol?
    Holoenzyme is required for transcription initiation Core RNA pol (after dissociation of sigma) continues with transcription
  41. No catalytic activity, but Helps RNA polymerase recognize specific promoters.act as ?global? transcription regulators in Bacteria, driving transcription of different sets of genes
    sigma factors
  42. What does Holoenzyme, core, sigma 70, sigma 54, and sigma 38 do?
    Hol recodnizes the promoters and initiates trans. Core catalyzes continued trans, 70 is house keeping genes, 54 nitrogen starvation genes, and 38 stationary phase genes.
  43. How is bacterial mRNA differant?
    No poly-A tail on 3? end, no 5? cap complexes in prokaryotic mRNAs. , a single mRNA may contain coding regions for multiple genes, i.e. polycistronic
  44. what is the shine-delgarno sequence?
    its the ribosome binding site. right before the translation start codon
  45. what are some of the regulation factors st the transcriptional level?
    Differnt sigma factors direct transcription, intrinisic regulation of sequence promoter, binding of regulatory proteins (activators or repressors), ATTENUATION and riboswitches.
  46. Premature termination of transcription due to formation of a terminator structure
  47. Binding of a metabolite to nascent mRNA (just beginning of transcription) resulting in premature transcription termination
  48. What are som reglations at the translation level?
    Secondary structure in 3' end of mRNA prevents degradation of message. Binding of regulatory protein to mRNA to prevent translation. Riboswitches: Binding of a metabolite to a complete mRNA that prevents translation. Antisense RNA binding to mRNA, which may prevent or allow translation
  49. what are some regulation at post translational level?
    Noncovalent binding of an affector molecule or regulatory protein to an enzyme (or other protein), affecting its function. Covalent modificatoin of an enzyme (or other protein), affecting its function e.g. phosphorylation, adenylylation
  50. prevent transcription when they are bound to DNA. Metabolites or other small molecules that affect repressor activity
    transcriptional repressors.
  51. promote/enhance transcription when they are bound to DNA. Metabolites or other small molecules that affect activator activity
    transcriptional activators
  52. bind to repressor proteins and prevent DNA binding/activity ---> lack of repression
    Transcriptional repressor inducers
  53. bind to repressor proteins and enhance DNA binding/activity ---> repression
    Transcriptional repressor corepressors
  54. bind to activator proteins and enhance DNA binding/activity ---> activation
  55. bind to the activator and prevent DNA binding/activity ---> lack of activation
  56. what are the three genes that code for the lac operon?
    lacZ, lacY, lacA
  57. encodes beta-galactosidase ? cleaves lac to glu and gal (also makes allolactose
  58. encodes a transmembrane lactose permease (transporter
  59. encodes galactoside transacetylase (function in lac catabolism unclear
  60. acts as the inducer for the LacI repressor, i.e. as a molecular signal for the presence of lactose
  61. Catabolite repression is achieved by a transcriptional activator
  62. Cyclic AMP receptor protein (CAP). Genes controlled by CAP require its binding at
    an activator site upstream of the promoter.
  63. To bind the activator site, CAP must first bind an inducer molecule
  64. cAMP is made from ATP by
    adeylate cyclase
  65. Adenylate cyclase activity is inhibited by
  66. As glucose is depleted, cAMP levels increase and CAP becomes
  67. lac genes are transcribed if
    lactose is present.
  68. Mechanism for cell density-dependent changes in gene expression/physiology. Functions by positive feedback mediated by an autoinducer (AI) molecule.
    Quorum sensin in bacteria
  69. What else does the Quorum sensing control?
    genes for aditional functions. Such as biolumenescence such as thye vibrio fischeri
  70. Explain the quorum sensing in the vibrio fisheri
    LuxR is the transcriptional activator, Autoinducer (AI) acts as the inducer, LuxR on its own is inactive. AI difuyses out of cell until it is high enough to bind to the LuxR. THese will then induce transcription of genes need for bioluminescence.
  71. What are the two compnents of the regulatory system?
    Sensor kinase and Response regulator.
  72. in the two component regulatory system where do they usually sense?
    Sensor kinase senses externall things and response regulator senses cytoplasmic item, internall.
  73. this differs from normal homologouf recombination. Shorter regions of homology are used. these are recognized by recombinase enzymes specific to these sites.
    Site-specific recombination.
  74. heritable change in DNA sequence
  75. This mutation is errors in replication, lesions in DNA, and action of mobile genetic elements or recombiunation.
    Spontaneous mutations
  76. these mutations are due to exposure to physical or chemicals.
    Induced nutations.
  77. What can cause induced mutations?
    base analogues, DNA modifying agents, intercalating agents, UV radiation or ionizing radiation.
  78. these miutations can be lethal and harmful effects on the cell
  79. have neither harmful or beneficial effects from mutation
    neutral mutations
  80. These mutations are rare and can result in helpful changes that can improve cell growth.
    Beneficial mutations
  81. are changes in DNA sequences at individual positions.are categorized by their effects on products
    point mutations
  82. what are some point mutations?
    missense, nonsense, and silent
  83. mutation that result in change in resulting protein sequence at a given amino acid position (i.e. a change resulting in a codon that codes for a different amino acid)
  84. muitation result in a premature stop codon ? truncated protein
  85. mutation that are a change to a codon that codes for the same amino acid
  86. Small insertions and deletions in a gene can result in a __________ that alters the reading frame and ?scrambles? the resulting amino acid sequence
    frameshift mutation
  87. insertions and deletions usually result in loss-of-function (or total loss) of a gene or genes where the mutation takes place
  88. are an additional type of mutation ?reversal? of DNA sequence between two sites Recombination and acquisition of new DNA can also result in mutations
  89. what are the two tyopes of reverant mutations?
    true reverant and second-site reverant
  90. If the back-mutation restores the original genotype as well, it is a
    true revertant
  91. If the mutation causing reversion is somewhere else, it is a
    second-site revertant
  92. Culture of a strain with a point mutation, e.g. in a histidine biosynthesis gene. This strain cannot grow in the absence of added histidine (His- phenotype), but is one point mutation away from being able to make its own (His+ phenotype). Plate onto minimal medium with small amount histidine (to allow minimal growth and chance for mutation to occur). Either add the suspected mutagen to the bulk agar medium or infused into a disk placed on a region of the plate. Increase in number of His+ revertants in the presence of the compound in question suggest that it is mutagenic
    the ames test
  93. Any transfer of DNA that results in organisms acquiring new genes that did not come directly come from parent organisms. Typically involves small pieces of DNA in the form of plasmids or chromosomal fragments. Readily occurs naturally, but is very useful in the laboratory as well
    Horizontal gene transfer
  94. Donor is lysed bacterial cell/ Defective bacterial phage is carrier of donor DNA. live recipient of cell so same species as a donor.
  95. Free donor dna fragmented go into live competent recipient cell.
  96. donor cell with pilus. fertility plasmid in donor and recipient alive. bridge forms between cells to trasnfer DNA.
  97. What is an example of using slectable markers.
    Find a suitable marker (amp reistance), a compatible host, and growth under selective conditions. (amps resistant cells growth on amp plate)
  98. give an example of a screeing method for mutations.
    complete mediuym used. plate put on stamp. Stamp used to innoculate minimal plates one compete and one missing something. Compair what grows and what doesnt.
  99. Make mutants of the microbe that are unable to degrade pectin, then find the gene(s) that were mutated (example using transposon mutagenesis)
  100. Take random fragments of genomic DNA from the microbe and introduce them into a microbe unable to degrade pectin, look for fragments that allow the new host to gain pectin degrading phenotype
    Molecular cloning and heterologous expression
  101. sequence the microbe?s genome, look for genes related to known pectin-degrading enzymes
    Genome sequencing
  102. What are the three key structural components of IS and transposons?
    Both contain genne coding for transposase, inverted repeats at the nd of the transposable element, and not capable of replication as extrachromosomal elements.
  103. what are the two essebntail features of a cloning plasmid?
    transposase gene and transposon
  104. are endonucleases that recognize specific DNA sequences and cleave DNA
    Restriction enzymes
  105. enzymes are useful for in vitro manipulation of DNA. Have become important tools in molecular biology and are widely available commercially
    Type II restriction enzymes
  106. This allows degradation of foreign (e.g. viral) DNA while leaving host DNA intact.Activity can be prevented by modification of DNA binding site
    methylation by a methylase. Genes for the restriction enzyme and corresponding methylase are often found together
  107. Permanent loss of reproductive capability, even under optimum growth conditions, has become the accepted microbiological definition of death
    the working definition of death in microbes
  108. what is meant by viable but not culturable?
    maintain membrane charge and some metabolism, cannot grow in normal medium, can be revived under certain conditions.
  109. : Complete removal or destruction of all viable microbes (including endospores
  110. Destruction or removal of vegetative microbes, but not endospores
  111. Related to disinfection, but not as ?strong?; Reduction of vegetative cells to an acceptable (low) number. E.g. pasteurization, cleaning of eating utensils in restaurants
  112. Chemicals used on body surfaces to destroy or inhibit vegetative microbes
  113. Chemicals used to kill or inhibit microbial growth inside the human body?e.g. antibiotics.
    antimicrobial chemotherapy
  114. why is killing endospores the gold standard?
    killing those means that you can kill everything smaller.
  115. Time required for a 90% decrease in viability is the
    decimal reduction time.
  116. What are some things to concider that will affect the ,icorbial death?
    Population size, composition, concentration of antimicrobial agent, exposure time, temperatiure adn pressure, and nature of the sample.
  117. Operates at lower temperatures and shorter exposure times to achieve the same effectiveness as dry heat. Microbicidal effect is the coagulation and denaturation of proteins. Also, destabilization of membranes.
    Moist heat
  118. Dehydrates the cell, removing water necessary for metabolic reactions; denatures proteins. At very high temperatures or prolonged exposure, dry heat oxidizes cells and cell components, burning them to ashes
    dry heat
  119. Which takes longer to sterilize, dry or moist heat?
    Dry heat
  120. what are some distinct differences between dry and moist heat?
    Dray takes lionger, higher temperatures can be used for dry heat, and dry heat does not need to be done at higher pressures.
  121. Shortest length of time required to kill all test microbes at a specified temperature
    thermal death time
  122. Very common method for sterilization in the laboratory and hospitals, both to sterilize media and instruments and to dispose of hazardous wastes. Essentially ?heavy duty pressure cooking?.Typically done at 121?C under 15 psi pressure (30 psi total pressure) for 15-40 minutes (20 minutes typical).What happens to liquid medium?why won?t it boil awayjQuery112408333479531883714_1540863470580?. Requires special instrumentation to maintain high temp. and pressure
  123. What are some examples of moist heat?
    Boiling water, tyndallization, and pasteurization
  124. Repeated exposure to steam (100?C) followed by cooling. The procedure is designed to kill vegetative cells and encourage spores to germinate during the cooling periods so they can then be killed in the next steaming step. Useful for media that is sensitive to autoclaving and cannot easily be filtered (e.g. has solid particles)
  125. Exposure of liquid to elevated (but not boiling) temperatures. Flash pasteurization: 71.6?C for 15 sec. Batch pasteurization: 63-66?C for 30 min. Commonly applied in the beverage industry
  126. Effective method to remove microbes from air and liquids. Fluid is strained through a filter with openings large enough for the fluid to pass, too small for microbes. Typically membrane filters with
    0.2 micrometer pore size
  127. Can low temperature, desiccation or osmotic pressure be used for sterilization or disinfection, or just to inhibit growth of (and often to preserve) microbes?
    yes just not very effective
  128. Gemicide that Can destroy vegetative cells, viruses; can destroy endospores with sufficiently long exposure
  129. Germicide that Can destroy vegetative cells & viruses, but not endospores
  130. germicide that Effective on some (but not all) vegetative cells and/or viruses
  131. WHat are some exaples of HIgh-intermediate germicides?
    Chlorine, iodine, H2O2, Aldehydes, and ethylene oxide (gas)
  132. What are some examples of Intermediate -low germicides.
    Phenol and other phenolics, chlorexidine, alcohols, detergents, and heavy metals.
  133. Alcohol-based solution rather than aqueous
  134. what does glycolysis produce?
    2ATP, 2NADH, and 2 Pyruvate
  135. what is the central molecule to respiration?
  136. Why is pyruvate the central molecule?
    because it is the product from glycolysis.
  137. What donates electrons is anaebolism?
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Micro exam 2
exam 2