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
162. Describe site-specific recombination
163. What are transposable elements
164. Describe simple transposons
165. Describe compound transposons
166. What are simple transposition
167. Describe replicative transposition
168. Describe bacterial plasmids
169. Describe the F factor
170. Describe bacterial conjugation
171. Describe F’x F’ mating
172. Describe conjugation machinery and the rolling circle mechanism
173. Describe the integration of F into the chromosome , generating Hfr;s
174. Describe hfr conjugation
175. Describe F’ conjugation
176. Describe bacterial transformation
177. What are the two types of bacterial transformation?
178. Describe natural transformation
179. Describe transformation by linear DNA
180. Describe transformation by a plasmid
181. Describe the DNA uptake in Bacterial transformation
182. Describe the DNA uptake in natural transformation
183. Describe artificial transformation
184. What is transduction
185. Describe generalized transduction
186. Describe specialized transduction
187. Describe antibiotic resistance
188. What are the two types of antibiotic resistance
189. Describe the mechanisms of acquired drug resistnace
190. What are immunity genes
191. Where can resistance genes be found?
192. What are R (resistance) plasmids
193. What are composite transposons
194. What are gene cassettes