1. Homework #1 is posted and due 9/20
Bonus #1 is posted and due 10/25

2. DNA contains the information to make RNA and/or proteins.
Fig 8.11
DNA contains the information to make RNA and/or proteins.
Protein

3. General model of Ca++ signaling

4. Ca++ is involved in signal transduction for responses of:
in Plants
Development
Cold
Guard cell closing
Osmotic shock
Light
Fungal infection
Touch
Pollen tube growth
Wounding…
in Animals
Neurons
Muscle movement
Wounding
Development
Fertilization
Hormones …
How can there be specificity?

5. Everything has its place…

6. 2 hypotheses about how Ca++ signals are transduced:
Signatures vs. Switches
Fig 1. Scrase-Field and Knight, Current Opinion in Plant Biology 2003, 6:500–506

7. Stomata regulate gas exchange: CO2 in, O2 and water out
H2O
H2O

8. Stomata
open
closed

9. Ca++ fluxes in guard cells in response to hormone or stress that cause stomatal closing.
Wildtype vs. det3 and gca2: mutants that fail to close stomata following treatment
Fig 5. Sanders et al., The Plant Cell, S401–S417, Supplement 2002

10. Stomata aperture in response to Ca++ spikes:
More spikes= more closing
Fig 1. Allen et al., Nature, Vol 411: , 28 June 2001

11. Spike timing is critical for response
Fig 2. Allen et al., Nature, Vol 411: , 28 June 2001

12. Duration of spikes for stomata closing
Fig 2. Allen et al., Nature, Vol 411: , 28 June 2001

13. 2 hypotheses about how Ca++ signals are transduced:
Signatures vs. Switches
Fig 1. Scrase-Field and Knight, Current Opinion in Plant Biology 2003, 6:500–506

14. Signal transduction
– such as changes in cellular components or production of new cellular components

15. How do cells express genes?
Fig 8.11
How do cells express genes?

16. The relationship between DNA and genes
Fig 8.3
The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA

17. Combinations of 3 nucleotides code for each 1 amino acid in a protein.

18. Fig 8.4
Overview of transcription
Figure 8-4

19. Each nucleotide carbon is numbered
Fig
Each nucleotide carbon is numbered

20. Fig 7.8
Each nucleotide is connected from the 5’ carbon through the phosphate to the next 3’ carbon.

21. Each nucleotide is connected from the 5’ carbon through the phosphate to the next 3’ carbon.
Fig 7.8

22. The relationship between DNA and RNA
Fig 8.6

23. What is so magic about adding nucleotides to the 3’ end?
Fig 8.4
What is so magic about adding nucleotides to the 3’ end?

24. How does the RNA polymerase know which strand to transcribe?
Fig 8.8

25. Reverse promoter, reverse direction and strand transcribed.
RNA 5’ 3’ 5’ 3’ 5’

26. Why do polymerases only add nucleotides to the 3’ end?
RNA
RNA
DNA
DNA U U

27. Hypothetically, nucleotides could be added at the 5’ end.
Incoming
nucleotide 5’
Hypothetically, nucleotides could be added at the 5’ end. 3’

28. Error P
P-P

29. The 5’ tri-P’s can supply energy for repair
Error P
The 5’ tri-P’s can supply energy for repair U
P-P-P P

30. Error repair on 5’ end not possible.
Incoming
nucleotide
Error repair on 5’ end not possible. 5’ 3’

31. Need for error repair limits nucleotide additions to 3’ end.
RNA
RNA
DNA
DNA U U

32. The relationship between DNA and genes
Fig 8.3
The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA

33. Promoter sequences in E. coli
Fig 8.7

34. Transcription initiation in prokaryotes: sigma factor binds to the -35 and -10 regions and then the RNA polymerase subunits bind and begin transcription
Fig 8.8

35. Transcription Elongation
Fig 8.9
Transcription Elongation

36. Termination of Transcription
Fig 8.9

37. Eukaryotic promoters are more diverse and more complex

38. Transcription initiation in eukaryotes
Fig 8.12
Transcription initiation in eukaryotes

39. Some genes code for RNA (tRNA, rRNA, etc) mRNA is used to code for proteins
RNA synthesis
Protein

40. rRNA is transcribed by RNA polymerase I

41. tRNA is transcribed by RNA polymerase III

42. mRNA is transcribed by RNA polymerase II

43. mRNA is processed during transcription and before it leaves the nucleus.
(transcribed from DNA)

44. Addition of the 5’ cap, a modified guanine
Fig 8.13

45. Addition of the 3’ poly-A tail
Fig 8.13
After the RNA sequence AAUAAA enzymes cut the mRNA and add 150 to 200 A’s

46. DNA Composition: In humans:
Each cell contains ~6 billion base pairs of DNA.
This DNA is ~2 meters long and 2 nm wide.
~3% directly codes for amino acids
~10% is genes
In a single human cell only about 5-10% of genes are expressed at a time.

47. mRNA is processed during transcription and before it leaves the nucleus.
(transcribed from DNA)

48. Splicing of introns
Fig 8.13

49. Conserved sequences related to intron splicing

50. Splicing an intron: intron removal.
Fig 8.16

51. Splicing an intron: reattach exons.
Fig 8.16

52. Some introns are self-splicing.
Fig 8.18

53. Was RNA the first biological molecule?
The RNA World pg 312 and more info in posted slides from 9/11

54. Theoretical evolution of self-replicating RNA

55. Hypothetical Origin of Life
pg 214

56. Alternate splicing of introns/exons can lead to different proteins produced from the same gene.

57. Complex patterns of eukaryotic mRNA splicing
(-tropomyosin)
Fig 8.14

58. Fruit fly DSCAM, a neuron guide,
115 exons over 60,000 bp of DNA
20 exons constitutively expressed
95 exons alternatively spliced
For over 38,000 possible unique proteins

59. Size and Number of Genes for Some Sequenced Eukaryotic Genomes

60. Some mRNAs are changed after transcription by guide RNA
RNA editing:
Some mRNAs are changed after transcription by guide RNA