1. Molecular Biology of the Cell
Alberts • Johnson • Lewis • Raff • Roberts • Walter
Molecular Biology of the Cell
Fifth Edition
Chapter 6
How Cells Read the Genome: From DNA to Protein
Copyright © Garland Science 2008

2. Chapter 6 How Cells Read the Genome: From DNA to Protein I) RNA
II) Eubacterial transcription
III) Eubacterial Initiation and Termination
IV) Eukaryotic polymerases
V) Eukaryotic Initiation
VI Elongation
VII Post-transcriptional modification (capping, splicing, cleavage and poly adenylation).

3. Graphical depiction of D. melanogaster chr 2
Figure 6-1 Molecular Biology of the Cell (© Garland Science 2008)

4. The Central Dogma
Figure 6-2

5. Gene regulation controls the expression of genes
Figure 6-3 Molecular Biology of the Cell (© Garland Science 2008)

6. The structures of ribose and deoxyribose
Figure 6-4a Molecular Biology of the Cell (© Garland Science 2008)

7. The structures of uracil and thymine
Figure 6-4b Molecular Biology of the Cell (© Garland Science 2008)

8. Uracil base pairs with adenine
Figure 6-5

9. RNA is single stranded and capable of folding
Figure 6-6 Molecular Biology of the Cell (© Garland Science 2008)

10. Figure 6-7 Molecular Biology of the Cell (© Garland Science 2008)

11. Table 6-1 Molecular Biology of the Cell (© Garland Science 2008)

12. snoRNAs modify rRNAs
Figure Molecular Biology of the Cell (© Garland Science 2008)

13. snoRNAs modify rRNAs
Figure Molecular Biology of the Cell (© Garland Science 2008)

14. E. coli RNA polymerase consists of 4 main subunits:
Beta, Beta’ and alpha(2)
omega
alpha

15. Transcription of two ribosomal RNA genes

16. The eubacterial transcription cycle
Figure Molecular Biology of the Cell (© Garland Science 2008)

17. Step 1: Core - sigma factor interact to recognize a promoter sequence
Figure 6-11 (part 1 of 7) Molecular Biology of the Cell (© Garland Science 2008)

18. Step 2: Open complex formation -- the DNA is melted
Figure 6-11 (part 2 of 7) Molecular Biology of the Cell (© Garland Science 2008)

19. Step 3: Abortive initiation
Figure 6-11 (part 3 of 7) Molecular Biology of the Cell

20. Step 4: Promoter clearance -- shift to elongation
Figure 6-11 (part 4 of 7) Molecular Biology of the Cell (© Garland Science 2008)

21. Step 5: Elongation
Figure 6-11 (part 5 of 7) Molecular Biology of the Cell (© Garland Science 2008)

22. Step 6: Termination signal
Figure 6-11 (part 6 of 7) Molecular Biology of the Cell (© Garland Science 2008)

23. Step 7: Release of mRNA
Figure 6-11 (part 7 of 7) Molecular Biology of the Cell (© Garland Science 2008)

24. The eubacterial transcription cycle
Figure Molecular Biology of the Cell (© Garland Science 2008)

25. E. coli RNA polymerase consists of 4 main subunits:
Beta, Beta’ and alpha(2)
omega
alpha

26. T. aquaticus RNA Polymerase

27. RNA polymerase
Figure 6-8a Molecular Biology of the Cell (© Garland Science 2008)

28. RNA polymerase structure

29. RNA polymerase structure
Figure 6-8b Molecular Biology of the Cell (© Garland Science 2008)

30. RNA polymerase structure

31. T7 RNA polymerase - single subunit

32. Multisubunit RNA polymerases may not be related to DNA polymerases and single subunit RNA polymerases
Figure Molecular Biology of the Cell (© Garland Science 2008)

33. Step 1: Core - sigma factor interact to recognize a promoter sequence
Figure 6-11 (part 1 of 7) Molecular Biology of the Cell (© Garland Science 2008)

34. Consensus sequences of the sigma70 promoter
Figure 6-12a Molecular Biology of the Cell (© Garland Science 2008)

35. Spacing of the sigma70 promoter
Figure 6-12b Molecular Biology of the Cell (© Garland Science 2008)

36. Variants of the sigma70 promoter region

37. The UP-element is recognize by the bacterial polymerase alpha subunit

38. Sigma70 contacts with the promoter DNA

39. E. coli sigma factors SIGMA FACTOR PROMOTER RECOGNIZED
70 (rpoD) most genes
38 (rpoS) stationary phase
32 (rpoH) heat shock
28 (rpoF) flagella
24 (rpoE) stress
54 (rpoN) nitrogen metabolism

40. The direction of transcription is determined by the promoter
Figure Molecular Biology of the Cell (© Garland Science 2008)

41. Transcription of the E. coli genome
Polycistronic mRNA
Figure Molecular Biology of the Cell (© Garland Science 2008)

42. Step 7: Release of mRNA
Figure 6-11 (part 7 of 7) Molecular Biology of the Cell (© Garland Science 2008)

43. An intrinsic terminator sequence creates a hairpin loop

44. Termination of transcription

45. Rho terminator

46. Table 6-2 Molecular Biology of the Cell (© Garland Science 2008)

47. RNA Polymerases
size Sulfolobus Saccharomyces cerevisiae Phage
(kDa) E. coli acidocaldarius Pol I Pol II Pol III mito T7
200 ’ 
100  50  20 10 4 13 14 12 17

48. Structure of eukaryotic RNA polymerase
Figure Molecular Biology of the Cell (© Garland Science 2008)

49. Pol II intitiation

50. Initiation of Pol II transcription is a complex process
Figure Molecular Biology of the Cell (© Garland Science 2008)

51. Figure 6-16 (part 1 of 3) Molecular Biology of the Cell (© Garland Science 2008)

52. Figure 6-16 (part 2 of 3) Molecular Biology of the Cell (© Garland Science 2008)

53. Figure 6-16 (part 3 of 3) Molecular Biology of the Cell (© Garland Science 2008)

54. Table 6-3 Molecular Biology of the Cell (© Garland Science 2008)

55. TBP bends DNA that it binds
Figure Molecular Biology of the Cell (© Garland Science 2008)

56. Pol II initiation sequences
Figure Molecular Biology of the Cell (© Garland Science 2008)

57. Enhancers can work from long distances to stimulate Pol II initation
Figure Molecular Biology of the Cell (© Garland Science 2008)

58. Pol II initiation is complex event

59. The mediator complex is conserved between yeasts and humans

60. Initiation of Pol I transcription Initiation of Pol III transcription

61. Elongation

62. Pol II undergoes modification during elongation

63. Phosphorylation of the CTD tail regulates the RNA polymerase

65. Transcription cause positive supercoiling ahead of the polymerase
Figure 6-20c Molecular Biology of the Cell (© Garland Science 2008)

66. Post-transcriptional modification of mRNA

67. Eukaryotic mRNAs undergo transcriptional processing
Figure Molecular Biology of the Cell (© Garland Science 2008)

68. Pol II transcripts are capped and poly adenylated
Figure 6-22a Molecular Biology of the Cell (© Garland Science 2008)

69. RNA processing factors associate with the CTD of pol II

70. CTD modifications attract different processing enzymes
Figure Molecular Biology of the Cell (© Garland Science 2008)

71. Pol II mRNAs are capped at their 5’ ends
Figure Molecular Biology of the Cell (© Garland Science 2008)

72. A 7-methyl guanine nucleotide forms the 5’ pol II mRNA cap
Figure 6-22b Molecular Biology of the Cell (© Garland Science 2008)

73. Many human genes contain multiple introns (and exons)
Figure Molecular Biology of the Cell (© Garland Science 2008)

74. Exon shuffling contributes to genetic innovation

75. Splicing removes introns as a lariat structure
Figure 6-26a Molecular Biology of the Cell (© Garland Science 2008)

76. Sequences within an intron are required for splicing

77. RNA splicing is a complex sequence of reactions
Figure Molecular Biology of the Cell (© Garland Science 2008)

78. Figure 6-29 (part 1 of 2) Molecular Biology of the Cell (© Garland Science 2008)

79. Figure 6-29 (part 2 of 2) Molecular Biology of the Cell (© Garland Science 2008)

80. ATP hydrolysis is required for RNA intron rearrangements
Figure 6-30a Molecular Biology of the Cell (© Garland Science 2008)

81. Yeast RNA splicing

82. Common splicing errors
Figure Molecular Biology of the Cell (© Garland Science 2008)

83. Figure 6-35 Molecular Biology of the Cell (© Garland Science 2008)

84. The exon definition hypothesis is a model for how exons are recognized in a mRNA
Figure Molecular Biology of the Cell (© Garland Science 2008)

85. Exons are usually short in humans flies and worms
Figure 6-32a Molecular Biology of the Cell (© Garland Science 2008)

86. Human introns tend to be fairly long
Figure 6-32b Molecular Biology of the Cell (© Garland Science 2008)

87. Alternative forms of splicing
Figure 6-34a Molecular Biology of the Cell (© Garland Science 2008)

88. Figure 6-34b Molecular Biology of the Cell (© Garland Science 2008)

89. Self-splicing introns don’t require proteins for removal
Figure Molecular Biology of the Cell (© Garland Science 2008)

90. RNA cleavage and poly adenylation

91. RNA cleavage and poly adenylation
Figure Molecular Biology of the Cell (© Garland Science 2008)

92. Steps of RNA cleavage and poly adenylation
Figure 6-38 (part 1 of 3)

93. Steps of RNA cleavage and poly adenylation
Figure 6-38 (part 2 of 3)

94. Steps of RNA cleavage and poly adenylation
Figure 6-38 (part 3 of 3)

96. Figure 6-40 Molecular Biology of the Cell (© Garland Science 2008)

97. Alternative splicing and poly adenylation can create many proteins from the same gene
Figure Molecular Biology of the Cell (© Garland Science 2008)

99. RNA processing

100. RNA processing; CTD

101. NOT COVERED mRNA export Noncoding RNAS Nucleolus Subnuclear structures

102. Review Questions:
What are the steps of spliceosomal removal of introns?
What are two mechanisms of preventing splicing mistakes?
What are the important features of the exon definition hypothesis?
What are the differences between group I and group II intron splicing?
What energy source is needed for spliceosomal splicing? What is it used for.
What do snRNAs do?
True or False There are over 50 spliceosomal proteins and each snRNA associates with at least 7 proteins?

103. Review Questions:
An RNA polymerase is transcribing a segment of DNA that contains the sequence 5’-GTAACGGATG-3’
3’-CATTGCCTAC-5’
If the polymerase is transcribing left to right what will the sequence of the RNA be?
Given the sequence RNA --CUUAUCCUCU
DNA --GAATAGGTGATGTC*A
If an RNA polymerase is stopped on the current template describe how you could walk the polymerase to the * position.