1. Exam #1 is T 9/23 in class
(bring cheat sheet)

2. How do cells control which genes are expressed?
DNA is used to produce RNA and/or proteins, but not all genes are expressed at the same time or in the same cells.
How do cells control which genes are expressed?
Protein

3. Response (change in cellular components and/or gene expression)
Signal Transduction
External
Stimulus
Internal
Effector…
Effector
Effector
Effector
Response (change in cellular components and/or gene expression)
Perception
(by receptor)
Stimulus

4. How do cells express genes?

5. The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA

6. Combinations of 3 nucleotides code for each 1 amino acid in a protein.
Fig 13.2
Combinations of 3 nucleotides code for each 1 amino acid in a protein.

7. Overview of transcription
Fig 12.2
Overview of transcription

8. Each nucleotide carbon is numbered
Fig 9.8
Each nucleotide carbon is numbered

9. Fig 9.22
Each nucleotide is connected from the 5’ carbon through the phosphate to the next 3’ carbon.

10. Fig 9.22
Each nucleotide is connected from the 5’ carbon through the phosphate to the next 3’ carbon.

11. The relationship between DNA and RNA
Fig 12.8
The relationship between DNA and RNA

12. What is so magic about adding nucleotides to the 3’ end?
Fig 12.8
What is so magic about adding nucleotides to the 3’ end?

13. How does the RNA polymerase know which strand to transcribe?
Fig 12.7

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

15. Why do polymerases only add nucleotides to the 3’ end?
RNA
RNA
DNA
DNA U U
similar to Fig 11.11

16. Error P
P-P

17. 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

18. Error repair on 5’ end not possible.
similar to Fig 11.11
Incoming
nucleotide
Error repair on 5’ end not possible. 5’ U 3’

19. Need for error repair limits nucleotide additions to 3’ end.
RNA
RNA
DNA
DNA U U
similar to Fig 11.11

20. When to express a gene is critical
promoter
coding region
terminator
non-gene
DNA

21. Promoter sequences in E. coli
Fig 12.5
Promoter sequences in E. coli

22. Transcription initiation in prokaryotes: sigma factor binds to the -35 and -10 regions and then the RNA polymerase subunits bind and begin transcription
Fig 12.7

23. Transcription Elongation
Fig 12.8
Transcription Elongation

24. Termination of Transcription
Fig 12.11
Termination of Transcription

25. Eukaryotic promoters are more diverse and more complex
Fig 12.13
Eukaryotic promoters are more diverse and more complex

26. in eukaryotes: transcription factors are needed before RNA polymerase can bind
Fig 12.14

27. Transcription overview
Fig 12.3
Transcription overview

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

29. rRNA is transcribed by RNA polymerase I

30. tRNA is transcribed by RNA polymerase III

31. mRNA is transcribed by RNA polymerase II

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

33. Addition of the 5’ cap, a modified guanine
Fig 12.23
Addition of the 5’ cap, a modified guanine

34. Addition of the 3’ poly-A tail
Fig 12.24
Addition of the 3’ poly-A tail
After the RNA sequence AAUAAA enzymes cut the mRNA and add 150 to 200 A’s

35. What do the cap and tail do?
(transcribed from DNA)

37. Luciferase Gene (from fireflies) Expressed in a Plant

38. 100%
4.7%
0.34%
0.22%

39. The cap and tail have overlapping and distinct functions
5’ untranslated region
3’ untranslated region
Protects from degradation/ recognition for ribosome
Protects from degradation/ transport to cytoplasm

40. 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.

41. Introns are spliced out of most mRNAs before they leave the nucleus.
(transcribed from DNA)

42. Sequences shown in bold are highly conserved
Conserved sequences related to intron splicing
Sequences shown in bold are highly conserved
Serve as recognition sites for the binding of the spliceosome

43. Splicing an intron: intron removal.
Fig 12.22

44. Splicing an intron: reattach exons.
Fig 12.22

45. Alternate splicing of introns/exons can lead to different proteins produced from the same gene.
Fig 15.16

46. Complex patterns of eukaryotic mRNA splicing
(-tropomyosin)
Fig 15.16

47. 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

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

49. Some mRNAs are changed after transcription by guide RNA
RNA editing:
Some mRNAs are changed after transcription by guide RNA
Tbl 12.3

51. A processed mRNA ready for translation
5’ untranslated region
3’ untranslated region

53. Exam #1 is T 9/23 in class
(bring cheat sheet)