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BIOL 438 Practice Exam 2 1. What are some examples of anabolism?

2. Why is sulfur assimilation important?

3. What are usable sulfur sources 4. What is the assimilatory sulfate reduction?

5. How is assimilatory sulfate reduction different from dissimilatory sulfate reduction?

6. Describe the process of assimilatory sulfate reduction.

7. Describe the amino acid biosynthesis – branching pathways.

8. Describe anaplerotic reactions and give examples 9. Describe the process of anaplerotic CO2 fixation 10. Describe the process of glyoxalate cycle.

11. Describe phosphorus assimilation 12. Describe purines and pyrimidines.

13. What are nucleosides and nucleotides?

14. Describe the process of purine biosynthesis.

15. Describe the process of pyrimidine biosynthesis.

16. What are the types of lipid synthesis?

17. Describe the fatty acid synthesis.

18. Describe triacylglycerols.

19. Describe phospholipids and how they are made.

20. Describe lipopolysaccharides (LPS) and how they are made.

21. Describe how LPS are inserted into the cell wall.

22. Bacteria can use many regulatory options that can occur at different levels. What are the different levels? It can also result in change in transcription or translation of genes or protein function in response to what?

23. The regulation or transcription initiation involves what two genes?

24. What are constitutive and regulated genes?

25. What are the two modes of transcriptional control?

26. What is negative control? What is positive control?

27. What is an operon?

28. What are structural and regulatory genes?

29. Change in transcription depends on what?

30. Transcription of an operon produces a what?

31. Describe polycistronic mRNA. 32. What are the important transcriptional regulatory sites in DNA sequence of operons?

33. What are promoters and operators?

34. What are the features of operons regulated by negative control?

35. Describe the basic scheme of negative control.

36. What is the lac (lactose) operon of E. coli?

37. Describe lactose catabolism.

38. Describe what the lac operon consists of.

39. Describe the lac repressor.

40. Describe the regulation of the lac operon when the lactose is absent 41. Describe the regulation of the lac operon when the lactose is present 42. What is the trp (tryptophan) operon of E. coli?

43. Describe the trp operon of E. coli.

44. What does the trp operon consist of?

45. Describe the regulation of the trp operon when tryptophan is plentiful.

46. Describe the regulation of the trp operon when tryptophan is not available (needs to be synthesized).

47. What is the difference between the regulation of the lac and trp operons?

48. What is the differences in terminology, reflecting differences in mechanisms of the trp and lac operon?

49. Describe the genetic test for whether an operon is regulated by negative control.

50. Describe the numbering of DNA bases in Operons 51. Describe operons regulated by positive control 52. Describe transcriptional activator proteins 53. Describe the metabolism of the L-Arabinose (ara) operon of E. coli 54. Describe the discovery of the positive control 55. Describe the ara operon and the regulation of AraC 56. Describe when arabinose is absent 57. What are the two parts of aral 58. Describe when arabinose is present 59. Describe what araO1 is 60. Describe the two component regulatory systems and the phosphorelay systems 61. What different responses is controlled by the two component regulatory systems 62. Describe the two proteins that is included in the prototypical two-component regulatory system 63. Describe the transmitter and receiver domains of the two components of the system 64. Describe the regulation of synthesis of outer membrane porin proteins and the porin protein functions 65. Describe the regulation of porin proteins by a two component signal transduction system 66. Describe the PhoR/PhoB system in E. coli 67. Describe the NtrB-NtrC two component signal transduction system.

68. How can transcription also be regulated?

69. Describe intrinsic transcription terminators 70. Describe the trp (tryptophan) operon of E. coli.

71. Describe trp operon attenuation 72. Describe attenuation control of the trp operon 73. Describe attenuation control of the his (histidine) operon 74. Describe riboswitches 75. Describe the riboswitch of the riboflavin (rib) biosynthetic operon of bacillus subtilis 76. How to regulate translation with riboswitches?

77. How to regulate translation by small RNA molecules ?

78. Describe global regulatory systems 79. What is regulon 80. What is modulon 81. What are the mechanisms used for global regulation 82. Describe the second messengers in Global control 83. Describe catabolite repression 84. Describe diauxic growth 85. Describe the central regulator of catabolic repression 86. Describe catabolic repression-regulated operons 87. Describe catabolite activator protein (CAP) 88. Describe CAP regulation of lac operon 89. Describe the regulation of the lac operon by the lac repressor and CAP 90. Describe CAP regulation of araBAD operon 91. How is the level of cAMP regulated? Describe the regulation of cAMP. 92. Describe stringent response 93. Describe the heat shock system 94. Describe the RNA polymerase 95. How are sigma factors regulated?

96. Describe molecular chaperones 97. Describe Quorum sensing 98. Describe sporulation in Bacillus sibtillis 99. Describe mutations 100.

What is a wild type?

101.

What is a mutant?

102.

What is phenotype 103.

What is genotype?

104.

What are alleles?

105.

What are spontaneous mutations 106.

What are induced mutations?

107.

What are forward mutations?

108.

What are reversion mutations 109.

What are suppressor mutation 110.

Describe point mutations 111.

Describe the mutations in essential genes 112.

Describe the temperature sensitive mutations 113.

What are the types of point mutations 114.

What are silent mutations 115.

What are missense mutations 116.

What are nonsense mutations 117.

Describe spontaneous mutations 118.

What are the types of base substitutions 119.

What are transitions 120.

What are transversions 121.

Describe deamination of cytosine

122.

Describe spontaneous hydrolysis of bases like depurination 123.

Describe tautomerization resulting transition mutations 124.

Describe induced mutations 125.

Describe methyl-nitrosoguanidine mutagenesis 126.

Describe thymine dimers 127.

What are methods of mutant isolation/detection 128.

What are auxotrophic mutations 129.

What are nutritional mutations 130.

Describe replica plating 131.

Describe the penicillin (or other B-lactam) Counter-selection or negative selection.

132.

Describe positive selection 133.

Describe carcinogenicity testing 134.

Describe DNA repair and list other repair systems 135.

Describe proofreading during DNA replication 136.

What are two examples of direct repair?

137.

Describe photoreactivation 138.

Describe correction of alkylated bases 139.

Describe mismatch repair 140.

How does mismatch repair system recognize which strand is the newly synthesized one?

141.

Describe methyl-directed mismatch repair in E. coli 142.

Describe excision repair 143.

List the types of excision repairs 144.

Describe base excision repair 145.

Describe nucleotide excision repair 146.

Describe recombinational repair 147.

Describe the SOS response and SOS regulon 148.

Why is the reversion frequency so much lower than the forward mutation frequency?

149.

Why does the ames test carcinogenicity use reversion rather forward mutation to quantify mutagenesis?

150.

What is recombination?

151.

What are the two modes of genetic transfer?

152.

Describe vertical gene transfer?

153.

Describe horizontal gene transfer 154.

What are merozygotes 155.

What are three modes of DNA exchange in Bacteria and Archaea?

156.

What are the possible fates of Donor DNA after HGT? 157.

What are the four types of recombination?

158.

Describe Homologous Recombination 159.

Describe holiday model of homologous recombination 160.

Describe recombinational repair 161.

Describe nonreciprocal homologous recombination

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Describe site-specific recombination What are transposable elements Describe simple transposons Describe compound transposons What are simple transposition Describe replicative transposition Describe bacterial plasmids Describe the F factor Describe bacterial conjugation Describe F’x F’ mating Describe conjugation machinery and the rolling circle mechanism Describe the integration of F into the chromosome , generating Hfr;s Describe hfr conjugation Describe F’ conjugation Describe bacterial transformation What are the two types of bacterial transformation?

Describe natural transformation Describe transformation by linear DNA Describe transformation by a plasmid Describe the DNA uptake in Bacterial transformation Describe the DNA uptake in natural transformation Describe artificial transformation What is transduction Describe generalized transduction Describe specialized transduction Describe antibiotic resistance What are the two types of antibiotic resistance Describe the mechanisms of acquired drug resistnace What are immunity genes Where can resistance genes be found?

What are R (resistance) plasmids What are composite transposons What are gene cassettes