microbiology final exam

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microbiology final exam
2013-12-12 02:41:55
sfsu microbiology exam

sfsu final exam microbiology
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  1. 3 characteristics of Transformation
    • Direct uptake of free DNA
    • translocasome takes up DNA
    • competence induced in different species
  2. 1 characteristics of Direct uptake of free DNA
    it needs competent cells in order to occur. They can be natural or artificial
  3. translocasome takes up DNA and is located in the nuclear envelope
  4. 3 characters in how competence is induced in different species
    • gram + cells secrete signals
    • has a competence factor
    • stress incudes competence (starvation)
  5. bacterial sex
  6. types of secretion system in conjugation
    type IV system (pilus)
  7. how conjugation works
    • pilus proteins encoded on F factor
    • transfers DNA on F factor (starts at oriT site)
    • recipient cell's transferred DNA forms a new F plasmid
    • recipient becomes donor
  8. conjugations requires the presence of special transferable plasmids
    ex F factor
  9. F factor
    fertility factor
  10. 2 sites of replication origins of F factor
    • oriV
    • oriT
  11. When is the replication site used
    • used in nonconjugating cells
    • used during DNA transfer
  12. conjugation begins with contact between the donor cell and recipient cell
    • F+ cell
    • F- cell
  13. plasmid transfer in conjugations requires specific genetic elements such as these 3
    • transfer region (tra)
    • origin of transfer (oriT)
    • F plasmid (fertility)
  14. when the F factor plasmid can integrate into the X, the cell is now a
    Hfr (high frequency recombination)
  15. this cell is capable of transferring X parts into a recipient cell
    Hfr cell
  16. 3 characters of Hfr cell transfer
    • genes transfer in order
    • entire X takes 100 min to transfer
    • the process can be used to map genes
  17. 3 characteristics of X mobilization
    • transfer is rarely complete
    • homologous recombo in the recipient cell following DNA transfer
    • diff Hfr strains - X mapping
  18. in Hfr, F factor integrates on bacterial X and tries to transfer entire X
  19. 2 characteristics of F' factor
    • F plasmid contains extra genes
    • Transfers extra genes to recipient
  20. how transduction works
    • virus injects DNA into cell (bacteriophage)
    • package DNA into viral capsid (contains package bac DNA by mistake)
    • transfer DNA to new host (can bring new bac genes to host)
  21. process in which bacteriophages carry host DNA from one cell to another
  22. 2 types of transduction
    • generalized transduction
    • specialized transduction
  23. this kind of transduction can transfer any genes from one donor to a recipient cell
    generalized transduction
  24. this kind of transduction can transfer only a few closely linked genes between cells
    specialized transduction
  25. 4 characters of defense against transferred DNA
    • bacteria cut entering DNA to pieces
    • bacteria add methyl groups to DNA
    • Entering DNA is destroyed
  26. bacteria cut entering DNA to pieces at specific restriction sites
  27. 2 reasons bac add methyl groups to DNA
    • prevents restriction at those sites
    • adds as cell replicates X
  28. in transferred DNA the entering DNA is destroyed unless these 2 occur
    • it comes from entering species
    • has methyl groups protecting DNA
  29. entering DNA replaces X DNA
  30. recombination occurs if
    sequence is overall very similar
  31. 3 ways DNA can enter the cell
    • transformation
    • conjugation
    • transduction
  32. 3 specific recombination proteins
    • RecA
    • RecBCD
    • RuvAB
  33. 2 reasons for recombo to occur besides DNA transfers
    • replaces variable sized section of DNA
    • repair damaged DNA
  34. Two different DNA molecules in a cell can recombine by these 2
    • generalized recombo
    • site specific recombo
  35. this kind of recombo requires that the 2 recombining molecules have a considerable stretch of homologous DNA sequences
    generalized recombo
  36. this kind of recombo requires very little sequence homology between the recombining DNA molecules
    site specific recombo
  37. how site specific recombo is diff from generalized
    it requires a short sequence recognized by the recombo enzyme
  38. heritable changes in DNA sequence
  39. this mutation is due to a change in one base pair
    point mutation
  40. point mutation
    transition ex
    transversion ex
    • purine>purine
    • pyrimidine>pyrimidine

  41. 3 examples of larger mutations
    • insertion of DNA into X
    • deletion of portion of the X
    • inversion flipping a portion of X
  42. 4 ways in which there is no effect of a mutation
    • mutations in regions between genes
    • "    " that change 3rd base of codon
    • "   " that change 1 amino acid into a similar one
    • "   " that change a protein that is not needed
  43. change in genotype
  44. effect of a mutation on an organism
  45. 4 different causes of mutations
    • spontaneous
    • induced by mutagens
    • electromagnetic radiation
    • chemicals
  46. single base change
    point mutation
  47. 5 types of mutations
    • silent
    • missense
    • nonsense
    • transitions
    • transversions
  48. insertions and deletion mutations are known as
  49. 4 types of mutations on a molecular basis
    • insertions/deletions
    • translocation
    • inversions
    • reversions
  50. suppressor mutations are known as
  51. 2 examples of electromagnetic radiation
    • xrays/gamma rays
    • UV light
  52. 3 characters to chemicals causing mutations
    • similarities of bases
    • base modifying
    • intercalators insert between bases
  53. chemical intercalators insert between bases causes what kind of mutations
  54. 2 types of DNA repair
    • error proof
    • error prone
  55. this kind of repair pathways prevents mutations
    error proof
  56. this kind of repair pathways risk introducing mutations
    error prone
  57. this repair operates only when damage is so severe that the cell undergoes apoptosis
    error prone repair
  58. examples of error proof repair
    Methyl mismatch repair; photoreactivation;   nucleotide excision repair; base excision   repair; and recombinational repair
  59. all microbial genomes have a mosaic nature
  60. transfer free DNA from environment
  61. DNA transfer after cell contact
  62. DNA transfer via bacteriophages
  63. restriction modification systems are used to
    protect bac from invasion by foreign DNA
  64. transposable elements include these 2
    • insertion seq
    • transposons
  65. genomes evolve primarily by horizontal gene transfer and by duplications follow by functional divergence through mutation
  66. 5 ways DNA repair occurs
    • mismatch repair
    • thymidine dimers
    • damaged bases
    • recombo repair
    • sos repair
  67. how does mismatch repair work
    • mispaired base cut out of strand
    • (strand w/o methyl groups is newer and assumed to be an error)
  68. nucleotide excision repair that is induced by UV
    thymidine dimers
  69. what cuts out the nucleotide in the excision repair
    UvrAB complex
  70. this DNA repair is excised by specific enzymes in damaged bases
  71. damaged bases are replaced by
    DNA pol I
  72. this kind of repair occurs after strand has replicated
    recombo repair
  73. when the strand is repaired in recombo it is copied and its catalyzed by RecA recombinase
  74. 3 characters of SOS repair
    • extensive DNA damage inactivates LexA
    • activation of many repair genes
    • rapid polymerization of DNA
  75. the rapid polymerization of DNA is error prone but better than no repair
  76. this mobile genetic element moves from one DNA molecule to another
    transposable elements
  77. this element can move within and between X
    transposable elements
  78. these are simple transposable elements containing transposase gene which is flanked by short inverted repeat sequences
    insertion sequence
  79. these are targets for the transposase enzyme
    insertion sequence
  80. IS elements can transfer by 1 of 2 mechanisms
    • replicative transposition
    • nonreplicative transposition
  81. are complex transposable elements that carry additional genes
  82. small changes in gene sequence
    • slow changes in a protein
    • generally no new functions created
  83. large changes in X occurs these 3
    • insertions of new material
    • duplications of genes
    • genome reduction
  84. large changes in X insertions of new material in genome evolution via
  85. duplications if genes causes
    the creation of new functions for the cell as long as copied gene maintains original function
  86. movement of genes between cells
    horizontal gene transfer
  87. transposons carry genes to X
  88. plasmid carries genes between cells
    without having to become part of X
  89. effects of gene transfer
    spreads useful genes among bac
  90. 3 ways the effects of gene transfer spreads useful genes among bacteria
    • antibiotic resistance genes
    • pathogenicity islands
    • genes to degrade special metabolites
  91. archaea share many genes with bacteria
    share other genes only with eukaryotes and midway between bac and eukary
  92. genes in one cell may not have been inherited from parents
    obtained instead from other bacteria
    bacterial species are related through lateral transfer as well as through parentage
  93. most cancer results from multiple mutations
  94. ames test uses bacterial strain auxotrophic for histidine
    has mutation in hisG gene and cannot grow unless histidine is supplied
  95. mutagen causes reversion
    changes  mutation to normal form (rare)
  96. more colonies on measurement of mutagens means
    stronger mutagen
  97. transposable elements can do these 3
    • insert into X
    • can jump from one site to another
    • can copy itself to a new site
  98. when transposable elements
    jump from one side to another its known as
    can copy itself to a new site is known as
    • non replicative transposition
    • replicative transpositions
  99. 4 characters of regulating gene expression
    • microbes respond to changing environment
    • sense environment
    • must transmit info to X
    • alter gene expression
  100. 2 ways microbes respond to the changing environment
    • alter growth rate
    • "   " proteins produced
  101. how microbes sense their environment
    they have receptors on cell surface
  102. the altering of gene expression in microbes leads to these 2
    • change transcription rate
    • change translation rate
  103. 5 ways microbes control gene expression at several levels
    • alterations of DNA seq
    • control of transcription
    • control of mRNA stability
    • translational control
    • posttranslational controls
  104. Cells use different mechanisms to sense and respond to conditions within or outside the cell.
  105. help a cell sense internal changes and alter its gene expression to match.
    Regulatory proteins
  106. lacZ gene encodes
    beta galactosidase
  107. lacY gene encodes
    lactose permase
  108. the product of lacZ and Y genes both need proteins to digest lactose
  109. 2 characters of E.coli lac operon
    • multiple genes transcribed from one promoter
    • both genes are transcribed together
  110. 3 things that sigma factors are controlled by
    • alternate transcription and translation
    • proteolysis
    • antisigma factors
  111. Small regulatory RNAs can bind to mRNA and help stabilize it or make it susceptible to degradation.
  112. bacteria can communicate with each other
    quorum sensing
  113. In quorum sensing, bacteria can communicate with each other at high cell densities via
  114. DNA microarrays (RNA) and two-dimensional gels (protein) provide global snapshots of expression
  115. The lacZYA operon is regulated as follows:
    • - Operon is off when LacI binds to the operator.
    •   - Operon is on when allolactose binds to LacI; cAMP-CRP are bound to the promoter (and there is no glucose around).
  116. The tryptophan operon is regulated by
    repression and attenuation (premature transcript termination).
  117. Induction of a quorum-sensing gene system requires the accumulation of a secreted small molecule called
  118. At a certain extracellular concentration, the secreted autoinducer reenters cells.
  119. autoinducer reenters cells.
      - It binds to a regulatory molecule. Once bound
    The LuxR-autoinducer complex then   activates transcription of the luciferase target   genes that confer bioluminescence
  120. 2 characters if quorum sensing
    • Cells work together at high cell density
    • Send signal chemical to other cells

  121. Cells work together at high cell density causes these 2
    • V. fischeri becomes bioluminescence
    • Many bacteria form biofilms
  122. Autoinducer chemical for V. fishcheri
    homoserine lactone
  123. when microbes send signal chemicals to other cells these 2 occur
    • chemical accumulation
    • binds to sensor in cell
  124. Chemical accumulation
    high cell density
  125. the binding to sensor in a cell in cell signaling does what
    sensor activates transcription
  126. this alloq bac to switch type of flagellum made
    phase variation
  127. In phase variation, the section of a X undergoes inversion in 2 orientations
    • 1- element promotes transcription (H2 flagellin produced)
    • 2- H2 is not transcribed (cell makes H1 flagellin instead)
  128. trp operon in a cell must make
    the amino acid tryptophan
  129. trp operon requires many proteins made from one operon
    when tryptophan is plentiful, the cell stops synthesis
  130. trp repressor must bind tryptophan to bind DNA
    its the opp of lac repressor
  131. sensor kinase protein in PM function
    binds to signal (food or chemical cue)
  132. sensor kinases activates itself via phosphorylation
  133. 2 component signal transduction 2
    • sensor kinases protein in PM
    • cytoplasmic response regulator
  134. 3 functions of cytoplasmic response regulator
    • takes phos from sensor
    • binds X
    • alters transcription rate of multiple genes
  135. since lactose cannot pass through PM what2 ways does it undergo to enter the cell
    • permease allows entry
    • PMF
  136. lactose must be converted to glucose to be digested, what enzyme converts lactose
  137. this repressor protein blocks transcription
  138. how LacI blocks transcription
    • repressor binds to operator
    • blocks sigma factor from binding promoter
  139. how the repressor responds to presence of lactose
    • binds inducer or DNA
    • adds lactose which causes repressor to fall off operator
  140. inducer of lac operon
  141. sigma factor guides RNA pol to initiate transcription at promoter
  142. 2 functions of sigma factors when it comes to proteins
    • help guide sigma factor to promoter
    • can block sigma factor from binding
  143. 3 characters when proteins can help guide sigma factor to promoter
    • activates
    • binds to DNA sites next to promoter
    • increase freq of that gene's transcription
  144. 3 characters when protein block sigma factor from binding
    • repressor
    • binds to DNA sites next to promoter (operator)
    • lowers freq of that gene's transcription
  145. this acts as repressor to block transcription
  146. 2 characters of ara operon
    • araC acts as repressor to block transcription
    • addition of arabinose changes conformation
  147. 2 occurances to when an addition of arabinose changes conformation on ara operon
    • acts as activator
    • stimulates binding of RNA pol
  148. is the easiest sugar to digest
  149. sugars converting to glucose require syn of proteins beta gala
  150. if glucose is present, lac operon is not transcribed
  151. how the presence of glucose affects signals inside cell 2
    • entry of glucose directly affects adenylate cyclase
    • lowers amount of cAMP
  152. high glucose = low cAMP
  153. CRP protein is what kind of protein
  154. 3 function of CRP protein
    • binds next to promoter
    • stimulates open complex
    • increases transcription of lac and other operon
  155. CRP responses to presence of cAMP
  156. what happens when CRP responds to presence of cAMP
    acts as activator only when bound to cAMP
  157. high glucose>low cAMP levels>CRP inactive
  158. When CRP is inactive, this happens
    does not bind to operons and has low levels of lac transcription
  159. trp operon weakening 3 steps
    • leader peptide on mRNA encodes 2 tryptophan
    • ribosomes binds to mRNA as transcription
    • stalled ribosomes prevents mRNA from forming a transcription termintor
  160. thiamine prevents translation of thiamine biosynthesis enzyme
    feedback inhibition
  161. translational control riboswitches function
    binding of small molecules to the upstream regions can also induce stem loop structures that interfere with translation of the mRNA
  162. small regulatory RNAs
    • Small RNAs regulate transcription, translation
    • RNA probably predates DNA and protein
    • Made from ribose, prevalent sugar
    • Some viruses have genome made only of RNA, no DNA
    • Some RNAs have catalytic activity
    • Major catalytic activity of ribosome is performed by RNA
  163. Antisense RNA base-pairs to mRNA
    Usually prevents translation
    Until removed via endonuclease
    Targets the mRNA for degradation
    Universal method of gene control—found
    in all creatures
  164. sigma factors regulate transcription of all genes
    control of ratio of sigma factor determines global control of protein synthesis
  165. sigma factor 70 function
    initiates transcription at most genes
  166. Bs sigma 28 function
  167. sigma 38
    stationary phase
  168. sigma 32 function
    heat shock and stress response
  169. sigma 28
    flagellar response
  170. this structure allows translation of sigma 32 only at high temperatures
    temperature sensitive mRNA
  171. this rapidly removes sigma factors
    the rapid turnover allows more exact control
    sigma 70 degraded rapidly at 42 C
  172. anti-sigma factors block sigma activity until needed and respond to the environment
  173. what are the 3 mechanisms that set the levels of a particular protein in the cell
    • transcription
    • stability of mRNA transcripts
    • translation of mRNA into protein
  174. researchers won a nobel prize for discovering that genes can be induced
    Jacob and monod
  175. what happens during phase variation
    a remodeling of an organism's DNA
  176. the protein product of the lacI gene is a
    regulatory protein
  177. one advantage to using sRNAs to control protein expression is that
    translation of the sRNA is not needed, thus saving amino acids
  178. lac operon will be maximally transcribed when this occurs
    lactose is present but not glucose
  179. an inducer causes gene expression by
    binding a repressor protein
  180. cAMP receptor protein has binding sites for
    the RNA pol alpha subunit
  181. cell function is regulated at what level
    both the biochemical and the genetic levels
  182. AraC is one of a large family of AraC-like proteins. what do all of the proteins have in common
    they all contain 2 helix turn helix DNA binding motifs
  183. this occurs in response to low energy stores
    stringent response
  184. what is composed of DNA
    operator (regulatory DNA sequence)
  185. when weakening occurs at the trp operon, when will the ribosome pause at the leader sequence
    when tryptophan levels are low
  186. lac operon includes which 3 proteins
    • lactose permease
    • B-galactosidase
    • transacetylase
  187. what technique can analyze proteome patterns
    2D gel electrophoresis
  188. accumulation of the heat shock factor, sigma H, increases at high temps because
    high temps sigma H mRNA adopts an unfolded secondary structure
  189. to get maximal expression of the lac operon, low glucose is
    necessary but not sufficient
  190. enzyme activity can be most rapidly changed at what level
    post translational modification of the enzyme
  191. ppGpp serves as a signal to the cell that
    ribosome synthesis should be curtailed
  192. similar to trp operon, genes encoding proteins for histidine synthesis are in a his operon that is under weakened control. The his operon leader seq probably
    contains adjacent codons for histidine
  193. trp operon are regulated by these 2
    • repressor protein
    • attenuation
  194. when glucose if present, enzyme IIA glc is not phosphor and LacY is inhibited
  195. these factors bind anti sigma factors, releasing sigma factors to activate transcription
    anti-anti sigma factors
  196. what may indicate a DNA site that binds a regulatory protein
    the DNA contain an inverted repeat
  197. proteome refers to
    complement of proteins present at a particular point of time
  198. some sRNA are responsible for
    regulating protein levels at the level of translation
  199. what functional group do kinases transfer to other molecules
  200. a DNA microchip, scanned with cDNAs, can give info about
    transcription of specific genes
  201. Acyl homoserine lactone produced by LuxI of vibrio is an example of
    an autoinducer
  202. AraC-like regulator differ from the LacI repressor in that
    only the AraC-like regulators can active transcription by direct interactions with RNA pol
  203. bacteria may dontate DNA to
    other bacteria of the same or of diff species, some eukary cells, and bacteriophages
  204. during DNA synthesis, if DNA polymerase incorporates a wrong nucleotide
    methyl mismatch repair will correct the unmethylated daughter strand to match the methylated template strand
  205. pathogenicity islands (PAIs) are often found intergrated near
    tRNA genes
  206. DNA encoding for which capability is part of the flexible gene pool
    antibiotic resistance
  207. the enzyme photolyase repairs DNA damage caused by
    UV radiation
  208. if a bacterial cell is missing AP endonuclease genes, what could not occur
    base excision repair
  209. if a bacterial cell is competent, it means
    the bacterium can import free DNA fragments and incorporate them into its genome
  210. a mutation always results in
    a change in genotype
  211. a bacterial strain lacking the RecA protein will be
    unable to perform generalized recombination
  212. what type of DNA uptake is dependent on viruses
  213. uptake of foreign DNA into a bacterium
    may help or harm the bacterium
  214. the relaxase enzyme, used during conjugation, has what enzymatic activity
  215. in the basic ames test for mutagenesis, a mutagen is tested to see if it can
    produce colonies on basic medium that lacks histidine, starting with a hisG mutant strain of bacteria
  216. an insertion sequence contains a gene for which enzyme
  217. one sign of horizontal gene transfer is
    a CG base ratio different from flanking chromosomal DNA
  218. which of the following is a laboratory technique for inducing transformation
  219. if a cytosine deaminates and becomes uracil, which enzyme will cleave the uracil from the DNA backbone in the first step of a repair process
  220. transduction is an example of
    horizontal gene transfer
  221. which type of DNA uptake is dependent on transferable plasmids
  222. which of the following enzyme is used in methyl mismatch repair, nucleotide excision repair and base excision repair
    DNA pol I
  223. in generalized recombination, which protein complex is responsible for homology searching
  224. overtime, the genome of a species
    may change due to mutation or gene swapping
  225. which of the following DNA repair mechanisms is error prone
    sos repair
  226. based on gel electrophoresis, a nonfunctional pro is found to have a smaller molecular weight than its wild type counterpart. A likely explanation for this observation is a
    nonsense mutation in the DNA coding for the protein
  227. what function do bacterial pheromones promote
  228. horizontal gene transfer can occur via these 3 ways
    • conjugation
    • transformation
    • transduction
  229. the process of importing free DNA from the environment into cells is called
  230. the mutation rate in a wild type E. coli cell is on the order of
    10^-6 base pair replicated
  231. this kind of recombination needs very little sequence homology between the donor and the recipient DNA
    site specific recombination
  232. transposable elements differ from plasmids in that
    only plasmids may exist autonomously, not integrated into host DNA
  233. how did so many different types of bacteria acquire such genomic blending? 3
    • heavy horizontal gene transfer
    • recombination events occurring w/in species
    • variety of mutagenic and DNA repair strategies
  234. reason for bac gene transfer
    acquire genes that might be useful as the environmental changes
  235. how to artificially manipulate the drive DNA into the cell like transformation?2
    • -use CaCl2 to alter the membrane which makes the cells electrocompetent which allows DNA to pass
    • -uses electroporation to shoot DNA across the membrane
  236. 3 reasons why species undergo natural transformation
    • import DNA may use the transformed DNA as food
    • use dead DNA seq that are compatible with their DNA to repair theirs
    • help species adjust to new environment
  237. vertical gene transfer is the same as cell division
  238. natural transformation in gram+ typically involves the growth phase depend assembly of a translocasome complex across the cell membrane
  239. this is composed of a binding protein that captures extracellular DNA floating in the environment
  240. once a translocasome is assembled, the cell can import free DNA fragments and incorporate them into its genome
  241. gram- are capable of natural transformation and do not make competence factors, why?
    they are either always competent or become when starved
  242. gram- organisms import DNA through type IV pilus assembly
  243. type IV pili assemble and disassemble at the cell surface expanding and contracting as a result. what does this do? 2
    • happens constantly during the growth of a culture
    • can help cells move across the solid surface
  244. specificity is due to particular sequences in DNA that are recognized by part of the uptake apparatus, but not all gram- competence systems display such specifics
  245. grams positives use nonpilis attachment proteins
  246. bacterial conju requires the presence of special transferable plasmids that contain all the genes needed for pilus formation and DNA export
  247. F factor contains 2 rep origins
    oriV and oriT on the plasmid
  248. plasmid
    oriV function
    oriT function
    • replicate and maintain the plasmid in nonconj cells
    • used to replicate DNA during DNA transfer
  249. plasmid can exist in extra chromosomal and integrated forms, this is called
  250. refers to the fact that there are more cells capable of transferring chromosomal DNA in a Hfr pop
    high frequency
  251. why a F- never becomes an Hfr when an Hfr undergoes conjugation with it
    the transfer never gets completed
  252. Hfr was used to determine map genes based on how long it took the genes to transfer
  253. the mapping process require mating an Hfr strain with a F- recipient that contained a mutation in the gene to be mapped. it is important in any genetic cross that the mutation create an observable phenotype
    if the mutation is repaired by conjugation and recombination, it will grow and form a colony on an agar plate lacking the mutated amino acid
  254. an aliquot of the mating mix is removed and the conjugation bridges are broken by blending
    interrupted mating
  255. The F factor derived from the plasmid that was inside of the chromosome (host DNA)
    F' factor
  256. F' plasmids do not have to recomb into the recipient X to be maintained, extra genes can be expressed a part of the F' plasmid
  257. extra genes can be expressed as part of the F' plasmid, this established merodiploid situation
  258. conjugal recipient of the F' factor contains 2 copies of those few genes, on the set of X and other on the F' factor
  259. the conjugal recipient's 2 copies of those few genes could be used to
    serve as raw material needed to evolve a new gene
  260. 1 group of plasmids that cannot transfer themselves can be mobilized if a transferable plasmid is also present in the same cell
  261. mobilizable plasmids usually contain this
    oriT like DNA rep origin recognized by the conjugation apparatus of the transferable plasmid. As a result when transferable plas begin conjugating so does the mobil plasmid
  262. antibiotic resistance genes on plasmids
    R factors
  263. mobilizable plasmids along with transferable plasmids is one way in which antibiotic resistance genes can spread throughout a microbe pop
  264. conjugation can be promoted by chem communication between cells
  265. plasmid pAD1 produces a prot called aggregation substance in which it
    catalyzes cell-cell contact and formation of conjug complex
  266. when pheromone molecules are release by bac, they are these and how do they work?
    • small pep
    • they enter the donor cell through oligopeptide permeases present in the mem. Once in donor, pher stimulates transcript of pAD1 genes
  267. Ti plasmid in the plant cell genome triggers the release of plant hormones that stimulate tumor growth of the plant. Plant cells within the tumor release this and do this
    • AA derivatives, opines
    • the microbe can then use as a source of C and N
  268. bacteriophages can accidently move bac genes between cells as an offshoot of the phage life cycle
  269. bac phages capable of gen transduc have trouble distinguishing their own DNA from that of the host when attempting to package DNA into their capsids. Host DNA gets packed in the phage capsid as well
  270. this defines the ends of the phage genome, marking where packaging system cuts the P22 DNA and starts packing DNA into next empty phage head
    pac site
  271. specialized or restricted transduction is a phage mediated gene transfer mech that resembles the formation of the F' factors
  272. how is specialized transduc diff from general
    specialized can only move a limited number of host genes
  273. specialized transduction will establish another merodiploid situation how
    the new recipient contains 2 copies of a host gene, one originally present on its X and one brought in by the transduc DNA
  274. safe sex approach to gene exchange
    restriction and modification
  275. the enzymatic cleavage of alien DNA and then protective methylation of self DNA
    restriction and modification
  276. Bac produce restriction enzymes that recognize short DNA seq and cleave DNA at or near those seq
  277. how do bac avoid committing suicide
    they protect themselves by produc matching modification enzymes that use S-adenosyl methionine to attach methyl groups to those same sex seq
  278. only one strand of a seq needs to be methylated in order to be protected from cleavage from restriction enzyme
  279. this type of restriction enzymes are used most for cloning and only possess endonuclease activity
  280. this type of restriction enzyme generally recognize palandromic
    type 2
  281. these 2 types of restriction enzymes have their restrict and mod activities in one multifunctional pro and cleave DNA from recog site
    type 1& 3
  282. if DNA is capable of autonomous replication
    if DNA is not
    • can coexist in cell sep from host X
    • degraded by nucleases
  283. kind of recomb requires two recomb molecules have a considerable stretch of homo DNA seq
    general recomb
  284. this recomb occurs via mech that requires very little sequence homology between the recomb DNA molecules
    site specific recomb
  285. this recomb requires a short seq recognized by recomb enzyme
    site specific
  286. a second CO that is some distance away from the first will lead to
    an equal exchange of DNA in which neither molecule increases in length
  287. 3 ways recomb is advantageous
    • DNA repair
    • repair damaged genes
    • enhance fitness
  288. RecA aka
  289. Before recA can find homology between 2 DNA molecules, the donor double stranded DNA molecule must
    be converted to a single strand
  290. the lacz+ gene product is normally used to
    catabolize the carbo lactose
  291. if lactose is the only carbo available the lacz mutant fails to grow
  292. radiation resistant radiodurans is thought to use RcA protein to patch together homologous ends of fragmented DNA in a way that reconstructs the X after extreme radiation damage
  293. phase variations are freq employed by pathogens to evade the host immune system by
    changing expression of cell surface pro
  294. a short 15bp seq known as the att site is present on these 2
    • lambda phage DNA
    • E.coli X
  295. this phage encoded protein engages the 2 att sites and through strand breakage and rejoining combines the molecule into 1
  296. a mutation that eliminates function
    knockout mutation
  297. spontaneous mutations are rare, and have a freq occurrence ranging from 10^-6 to 10^-8 per gen
  298. this is a change in bonding properties of amino and keto groups
    tautomeric shifts
  299. a spon mutation can arise from tautomeric shifts in the chem structure of the bases
  300. purine are particularly susceptible to spon loss from DNA by breakage of glycosidic bond connecting the base to sugar backbone. the result of this loss is formation of an apurinic site
  301. apurinic
    one missing purine
  302. DNA damage can occur as result of metabolic activities of the cell that produce intermediates such as H2O2, etc
    reactive oxygen species
  303. naturally occurring intracellular methylation agents can spontaneously methylate DNA to produce a variety of altered bases
  304. mutagens tend to increase the mutation rate by increasing the # of mistakes in a DNA molecule as well as by inducing repair pathways tat themselves introduce mutations
  305. mutation rate for a given gene
    # of mutations formed per cell doubling
  306. tells you how many mutant cells are present in a pop
    mutant freq
  307. ratio of mutants per total cells in a pop
  308. when a yeast cell rep to form a colony, a spon mutant yeast is unable to metabolize a compound which then accumulates and turns red
  309. microbial survival depends on
    its ability to repair
  310. types of repair mech depends on 2 things
    • type of mutation needing repair
    • the extent of damage involved
  311. some repair mech exise whole fragment og DNA or precisely excise the damaged bases or reverse them
  312. if there has been extensive damage of DNA,
    special emergency DNA polmerases are expressed that sacrifice rep accuracy to rescue the damaged genome
  313. how can a cell repair a mutation after it has been introduced during rep
    methyl mismatch repair which is base don recog of the methylation pattern in DNA bases
  314. Dam methylates the palindromic seq GATC to produce GAmeTC
  315. the pyrimidine dimers that form as a result of ultraviolet irradiation can be repaired by light activating mech
  316. photoreactivation function
    • photolyase binds to the dimer and cleaves the cyclobutane ring linking the 2 adjacent damaged nucleotides.
    • can be repaired without excising
  317. this operates in the dark and is used to excise other kinds of damaged DNA as well as pyrimidine dimers
    nucleotide excision repair
  318. this 3 subunit exonuclease excises a patch of 12-13 nucleotides that includes the dimer
  319. An RNA polymerase that encounters a UV dimer orother unrecognizable base on a template DNA strand willstall during transcription. The stalled RNA polymeraseis then recognized by a protein that mediates a processcalled transcription-coupled repair. The transcriptioncoupledrepair protein then snares a nearby UvrAB tobegin nucleotide excision repair.
  320. examples of error proof pathways
    • mismatch
    • photoreactivation
    • nucleotide excision
    • base excision