1. Exam #1 is T 2/17 in class (bring cheat sheet)

2. Protein 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?

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

4. How do cells express genes?

5. a gene The relationship between DNA and genes promotercoding regionterminatornon-gene DNA

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

7. Overview of transcription Fig 12.2

8. 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

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

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

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

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

16. P Error P-P

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

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

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

20. a gene When to express a gene is critical promotercoding regionterminatornon-gene DNA

21. Promoter sequences in E. coli Fig 12.5

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

24. Termination of Transcription Fig 12.11

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

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

27. Transcription overview Fig 12.3

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

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

34. Addition of the 3’ poly-A tail Fig 12.24 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. 4.7%0.34%0.22%100%

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

40. mRNA 5' 3' The 5' and 3' ends of the mRNA overlap.

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

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

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

44. Splicing an intron: intron removal. Fig 12.22

45. Splicing an intron: reattach exons. Fig 12.22

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

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

48. 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

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

50. RNA editing: Some mRNAs are changed after transcription by guide RNA For extra info about RNA editing see: http://www.cc.ndsu.nodak.edu/instruct/ mcclean/plsc731/genome/genome9.htm http://users.rcn.com/jkimball.ma.ultrane t/BiologyPages/R/RNA_Editing.html Tbl 12.3

51. Changes to mRNA prior to leaving the nucleus

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