1. Regulation of Gene Expression What are some benefits of regulating gene regulation?

2. What novel features of viruses and bacteria are relevant to learning about gene regulation and ultimately to controlling or changing it ourselves?

3. Regulation of Gene Expression Key Concepts Several Strategies Are Used to Regulate Gene Expression Many Prokaryotic Genes Are Regulated in Operons Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes Eukaryotic Gene Expression Can Be Regulated after Transcription

4. Regulation of Gene Expression Negative regulation(Repressor genes) Genes are turned off. or Positive regulation (Inducible genes) Genes are turned on.

5. Figure 11.2 Positive and Negative Regulation (Part 1)

6. Figure 11.2 Positive and Negative Regulation (Part 2)

7. Regulation can occur: Prior to transcription During Transcription After Transcription, before Translation During Translation After Translation

8. Figure 11.1 Potential Points for the Regulation of Gene Expression

9. Review the actions of viruses Lytic cycle: Lysogenic cycle:

10. Figure 11.3 A Gene Regulation Strategy for Viral Reproduction Gene Regulation by Viruses – used to take over cellular “machinery” to reproduce virus. Bacteriophage – Lytic cycle  Virus has a promoter that binds to RNA polymerase causing the transcription of some of its own genes. Protein products shut down host genes (degrade DNA or interfere post- transcriptionally), also stimulate production of viral genome replication and transcription. (will actually use nucleotides from degraded host DNA).

11. Figure 11.4 The Reproductive Cycle of HIV HIV – Retrovirus – Reverse transcriptase is used to make DNA from an RNA template. In turn, the viral DNA integrates into the host DNA (provirus- lysogenic cycle). Triggering event initiates the lytic cycle. TAT (transActivator of transcription) keeps host cell from mounting a defense to stop viral transcription. As virus leaves host cell it incorporates itself in a phospholipid membrane from the cell (a further deterrent to viral destruction)

12. Figure 11.5 Regulation of Transcription by HIV Made in its entirety

13. Figure 11.5 Regulation of Transcription by HIV mRNA transcription terminated early

14. Figure 11.6 Two Ways to Regulate a Metabolic Pathway Gene Regulation in Prokaryotes We have already learned how enzyme activity can be regulated through feedback systems. Regulation of enzyme activity is another method cells may employ.

15. E. coli in the gut can undergo a rapid change in gene production to exploit changing food source ex. Glucose  lactose. Three enzymes (β-galactoside permease, β-galactosidase, β-galactoside transacetylase) needed for lactose digestion are normally present in very small amounts. With the presence of lactose, these enzymes can be made 1000’s of times over within as little as 10 minutes.

16. Operons – units of transcriptional regulation consisting of promoter & operator sequences, plus structural genes. Usually upstream from the operon are DNA sequences to promote and transcribe a repressor protein.

17. lac operon- an inducible operon Normally the repressor protein is present in the cell and physically binds to the operator site, preventing transcription.

18. Figure 11.8 The lac Operon: An Inducible System (Part 2) The inducer (in this case allolactose –lactose isomer) binds to the repressor, releasing it from the operator, allowing transcription of the genes z,y,a for the production of the lactose digesting enzymes.

19. Figure 11.9 The trp Operon: A Repressible System (Part 1). trp operon – a repressible operon Normally the structural genes (which are used to synthesize tryptophan) for this operon, are operational. These genes are repressed when tryptophan is readily available to the bacteria from the environment. A corepressor (tryptophan) binds to the repressor, altering its shape so that it binds to the operator region of the DNA sequence. This then stops the transcription of the structural genes and tryptophan synthesis is halted.

20. Figure 11.9 The trp Operon: A Repressible System (Part 2)

21. What type of feedback is demonstrated upon the structural genes in each “operon” case? lac operon demonstrates positive feedback trp operon demonstrates negative feedback May be inducible (generally control catabolic pathways) repressible (usually control anabolic pathways) Most inducible operons are like the lac operon. Therefore, what type of pathway do inducible operons generally control: Anabolic or Catabolic?

22. Global gene regulation – Sigma factors - Proteins that can bind to RNA polymerase and direct it to specific promoters located in various locations throughout the bacterial genome in order to initiate transcription. This is useful when conditions warrant more than one related function to be carried out in a cell. Each set of genes rely on the same promoter. (Also found in eukaryote cells however, eukaryotic cells do not necessarily have functionally related genes clustered together, thus sigma factors may work between several chromosomes)

23. DO NOW Get a “do now” slip and Briefly describe how lactose influences the lac operon.

24. Gene Regulation in Eukaryotes Prior to transcription Cell signaling – Extracellular  initiation of signal transduction pathway from ligand binding to Receptor Intracellular  cellular environment triggers gene production ex. Cyclin Chromatin remodeling – Nucleosome consists of negatively charged DNA wrapped around 8 positively charged histone proteins which prevents DNA unwinding. Various enzymes (influenced by chemical environment) can change the interactions, causing nucleosomes to unwind.

25. In-Text Art, Ch. 11, p. 219 (1)

26. Figure 11.15 Epigenetic Remodeling of Chromatin for Transcription

27. DNA methylation – cystosine modification w/methyl group (heterochromatin vs. euchromatin) Ex. Barr body formation (X inactivation) Histone modification – methylation or phosphorylation - similar to above These can actually cause epigenomes of monozygotic twins to differ over time, causing different gene expression. Ex. One twin gets cancer.

28. Figure 11.13 DNA Methylation: An Epigenetic Change (Part 1)

29. Figure 11.13 DNA Methylation: An Epigenetic Change (Part 2) CpG islands (DNA regions rich In C and G doublets are areas Often heavily methylated. Upon replication, the new strands are unmethylated. New strands are then methylated, preventing transcription. Demethylation occurs when transcription is required.

30. Figure 11.14 X Chromosome Inactivation Barr Body

31. During Transcription Transcription factors  promoter binds to specific DNA sequence (enhancer) to begin ex. TATA  repressor binds to specific DNA sequence (silencer) to stop Sigma factors - coordinate the expression of several related genes, even on different chromosomes. For instance – drought response in plants requires conservation of water, protection from excessive salt in soil. All genes are activated to initiate a stress response.

32. Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 1) First transcription factor binds to the promoter…. …another joins it.

33. Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 2) Other factors and RNA polymerase bind to DNA Transcription is ready to begin.

34. In-Text Art, Ch. 11, p. 216

35. Figure 11.11 A Transcription Factor Protein Binds to DNA DNA is then bound to transcription factor. Transcription factor recognizes DNA sequence adjacent to promoter.

36. Transcription factors activated by change in cellular environment…. ….bind to DNA….. …proteins produced to deal with stress. Figure 11.12 Coordinating Gene Expression

37. After Transcription, before Translation RNA processing  unmodified GTP cap – oocyte – modified after fertilization thus transcription held until fertilization occurs.

38. Figure 11.16 Alternative Splicing Results in Different Mature mRNAs and Proteins Alternative splicing  same gene, different RNA due to different intron excision, resulting in different proteins Original estimation of genes was 80-100,00 now scaled back to @ 25,000….can you explain why?

39. microRNA – approx. 25 base nucleotides made from what was formally thought to be noncoding or junk DNA siRNA – Short interfering RNA -  Both target and degrade RNA ex. Transitional stage of larva Translational repressor proteins –RNAses

40. During Translation Length of Poly A tail determines mRNA stability preventing degradation, therefore translation continues. Location/chemical environment – influences embryo development –cell differentiation

41. Figure 11.19 A Proteasome Breaks Down Proteins After Translation Binding to ubiquitin  recognized by proteasome complex resulting in hydrolyzed protein

42. Protein not modified to finished product – proteolysis (proteases cleave protein), glycoylation and phosphorylation do NOT take place. Suggest detailed reasons why a protein may not be modified to its finished product.