1. Regulating Gene Expression
Homework #2 is posted and due 10/18
Exam key is posted

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

3. Exons are a very small part of DNA

4. Each step in gene expression presents an opportunity to regulate when and how much of a gene product will be produced.

5. Why change gene expression?
Different cells need different components
Responding to the environment
Replacement of damaged/worn-out parts

6. Two points to keep in mind:
Cellular components are constantly turned-over.
Gene expression takes time:
Typically more than an hour from DNA to protein. Most rapidly 15 minutes.

7. Blood clotting must happen within minutes

8. mRNA levels change in response to cold acclimation
Fowler and Thomashow
The Plant Cell, Vol. 14, , 2002

9. DNA damage inhibits rRNA transciption
Fig 1a
The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks Nature Vol 447 pg (7 June 2007)

10. Gene expression can be controlled at many points between DNA and making the final proteins.
Changes in the various steps of gene expression control when and how much of a product are produced.

11. In bacteria, transcription and translation occur simultaneously
In bacteria, transcription and translation occur simultaneously. So most regulation of gene expression happens at transcription.
Fig 8.11

12. 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

13. Operon: several genes whose expression is controlled by the same promoter
Fig

14. E. coli lactose metabolism
Fig 10.5
E. coli lactose metabolism

15. In the absence of lactose, the lac operon is repressed.
Fig 10.6
In the absence of lactose, the lac operon is repressed.

16. Fig 10.6
Lactose binds to the repressor, making it inactive, so that transcription can occur.

17. Fig 10.6

18. Glucose is a better energy source than lactose
Fig 10.13

19. Low glucose leads to high cAMP
cAMP binds to CAP which increases lac operon transcription
Fig 10.13

20. High glucose leads to low cAMP
low cAMP, CAP inactive, low lac operon transcription
Fig 10.13

21. The lac operon: one example of regulating gene expression in bacteria
Fig

22. Overview of transcriptional regulation
Figure 11-2
Fig 11.2

23. Mutations in the promoter show critical nucleotides
Fig 11.4

24. Gene Expression is controlled at all of these steps: DNA packaging
Transcription
RNA processing and transport
RNA degradation
Translation
Post-translational
Fig 16.1

25. Different levels of DNA packaging
Fig 11.10
Different levels of DNA packaging

26. Tightly packaged DNA is unavailable
Tightly packaged DNA is unavailable. DNA packaging changes as the need for different genes changes.

27. Histones can be post-translationally modified, which affects their abililty to bind DNA.
Fig 11.12

28. Acetylation (-COCH3): post-translational modifications of the histones loosen DNA binding

29. Acetylation of histones (-COCH3) causes a loosening of the DNA/histone bond…unpackaging the DNA.

30. Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Triennial Issue of 'Chemistry and Engineering’ DOI: /rsta
Published: September 13, 2007

31. Four-stranded DNA forms between sequences of guanines…G-quadruplexes
4 strand DNA Fig 1

32. Four-stranded DNA forms between sequences of guanines…G-quadruplexes
4 strand DNA Fig 1

33. The G-quadruplexes can form from 4, 2, or 1 DNA strand.
4 strand DNA Fig 2

34. During DNA replication, the ends of the DNA are not completely copied.
Fig 7.11

35. Telomeres are non-gene DNA at the ends of DNA strands.
Telomeres are shortened during DNA replication.

36. Telomeres can be lengthened by telomerase.
Fig 7.26

37. The telomeric cap structure is one place where G-quadruplexes can be found

38. Telomeres are non-gene DNA at the ends of DNA strands.
Short telomeres will cause cells to stop replicating or cell death.
The critical size is unknown.

39. Drugs that can block the action of telomerase, by binding the G-quadruplexes, are being investigated to treat cancer.

40. Eukaryotic promoters often contain G-rich areas
Fig 11.3

41. G-quadruplex in promoters
4 strand DNA Fig 5

42. If the promoter is defined as 1 kbase upstream of the transcription start site:
Quadruplex motifs are significantly overrepresented relative to the rest of the genome, by almost an order of magnitude.
almost half of all known genes have a putative quadruplex-forming motif
By comparison, the TATA box motif—probably the best-known regulatory motif and a staple of undergraduate textbooks—is found in only approximately 10% of genes.
Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: /rsta Published: September 13, 2007

43. Oncogenes, the genes involved in cancer, are especially rich in potentially regulatory quadruplexes—69% of them have such motifs
Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: /rsta Published: September 13, 2007

44. Werner syndrome, which causes premature aging, is caused by the lack of a helicase that binds to G-quadruplexes.
Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: /rsta Published: September 13, 2007

45. G-quadruplex ligands G-quadruplex TMPyP4 BRACO-19
Down regulates telomerase and some oncogene transcription
G-quadruplex
telomestatin
4 strand DNA Fig 6
Specifically binds to telomeres, naturally occurring in Streptomyces anulatus

46. Model of specific G-quadruplex ligand binding to G-quadruplex and a specific DNA sequence
4 strand DNA Fig 7