Gene Expression...What’s that?

1. Gene Expression...What’s that?

2. Identical twins share the same DNA but are they exactly identical? How might they be different? WHY????

3. Let’s read an article 

4. How do we regulate the expression of our genes?

5. Gene Regulation http://education-portal.com/academy/lesson/regulation-of-gene-expression-transcriptional-repression-and-induction.html#lesson

6. Involved in gene expression • DNA regulatory sequences • Regulatory genes • Small regulatory RNAs

7. Regulatory sequences • Stretches of DNA that interact with regulatory proteins to control transcription. Regulatory genes • A sequence of DNA encoding a regulatory protein or RNA.

8. Gene Regulation among bacteria • Bacteria cells are able to express the genes whose products are needed by the cell. • EX: need for tryptophan. • Have both positive & negative control mechanisms

9. -Expression of specific genes can be turned “on” by the presence of an inducer or can be inhibited by the presence of a repressor. -Inducers & repressors are small molecules that interact with regulatory proteins &/or regulatory sequences.

10. Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control). Regulatory proteins stimulate gene expression by binding DNA & stimulating transcription (positive control) or binding to repressors to inactivate repressor function. Some genes are continuously expressed; they are always turned “on” EX: ribosomal genes

11. Operons are one way in which genes are regulated.

12. The switch is the operator (segment of DNA) -it controls the access of RNA polymerase to the genes - Regulatory proteins stimulate gene expression by binding to DNA & stimulating transcription (positive control) or binding to repressors to inactivate repressor function. Operon= the operator, promoter, & genes they control –the entire stretch of DNA required for enzyme production for the tryptophan pathway.

13. Which do you think is more common for each type of operon- the gene in its non-repressed state?/ in its repressed state? Inducible operons are more commonly found in the repressed state while repressible operons are more often actively transcribing, thus are not repressed

14. Which type of operon would be used for anabolic reactions (making new molecules)? Repressible operons that are turned off when there is an excess of gene production

15. Which type of operon would be used for catabolic reactions (breaking down of molecules)? Inducible operons that are only turned on in the presence of the a substance produced by metabolism (metabolite).

16. Two types of Negative Gene Regulation • Repressible Operon: transcription is usually on but can be inhibited (repressed) when a specific small molecule binds to a regulatory protein. • EX: tryptophan • Inducible: usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein. • EX: lac operon (lactose) http://biology-animations.blogspot.com/2007/11/lac-operon-animation.html

17. What’s Going On??

18. Positive Gene Regulation When glucose is in short supply as an energy source, E. coli will use lactose. E. coli will then synthesize high quantities of the enzymes to breakdown the lactose. How does the cell sense a shortage of glucose? cAMP accumulates when glucose is scarce. cAMP binds with CAP (the activator & regulatory protein) & stimulates the transcription of a gene cAMP binds to CAP & CAP assumes its active shape. CAP attaches to the promoter which stimulates gene expression.

19. If the amount of glucose increases the cAMP concentration falls & therefore CAP detaches from the operon. The lac operon is under negative regulation by the lac repressor & positive regulation by CAP.

20. Can you hypothesize some other ways that might increase or completely shut down the transcription of a gene? EX: activators that help the RNA polymerase have greater affinity with the promoter region.

21. What differences in gene regulation might we see in the eukaryotic genes?

22. Consider the cells that are in the tissue of your big toe. Which genes are those cells going to need to use? How much DNA will be present in a given cell that won’t be used at any point except when the cell replicates? 95-97% of the genome of any given cell goes untranscribed When a cell receives a signal to transcribe specific genes, what facilitates its search for the genes? DNA is organized very precisely on a scaffolding of proteins that attach to nuclear lamina & cytoskeleton, thus every part of every strand is in a known location.

24. Each “bead” is a nucleosome. -the basic unit of DNA packing The looped domains coil & fold forming the characteristic metaphase chromosome

25. Gene expression in eukaryotes is controlled by a variety of mechanisms that range from those that prevent transcription to those that prevent expression after the protein has been produced. 5 kinds of general mechanisms that can be used. Transcriptional - These mechanisms prevent transcription. Posttranscriptional - These mechanisms control or regulate mRNA after it has been produced. Translational - These mechanisms prevent translation. They often involve protein factors needed for translation. Posttranslational - These mechanisms act after the protein has been produced.

26. Gene expression can be regulated at any stage, but the key step is transcription • All organisms • Must regulate which genes are expressed at any given time • During development of a multicellular organism • Its cells undergo a process of specialization in form and function called cell differentiation

28. Why is it an evolutionary advantage to be able to turn some genes off temporarily or permanently? Having genes that are always turned on when the gene product is not needed would be wasteful & use up the resources within a cell. Why are “volume controls” an advantage? Some gene products are in very high demand & need to have a greater number of transcriptions made so that the cell can function efficiently.

29. Signal NUCLEUS Chromatin Chromatin modification: DNA unpacking involving histone acetylation and DNA demethlation DNA Gene available for transcription Gene Transcription Exon RNA Primary transcript Intron RNA processing Tail mRNA in nucleus Cap Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Degradation of mRNA Translation Polypetide Cleavage Chemical modification Transport to cellular destination Active protein Degradation of protein Degraded protein Many key stages of gene expressioncan be regulated in eukaryotic cells

30. Regulation of Chromatin Structure & Histone Modifications Can affect the configuration of chromatin and thus gene expression

31. DNA Methylation The addition of methyl groups to certain bases (usually cytosine) in DNA is associated with reduced transcription in some species. Genes that are not being expressed have a tendency to be heavily methylated Removal of the extra methyl groups can turn on certain genes. Experiments have shown that deficient DNA methylation due to lack of a methylating enzyme leads to abnormal embryotic development. In these cases, DNA methylation is essential for the long-term inactivation of certain genes.

32. Epigenetic Inheritance Chromatin modifications don’t necessarily involve a change in DNA and yet they may be passed on from parent to offspring The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called: Epigenetic Inheritance

33. upstream The rate of gene expression can be increased or decreased by the binding of specific transcription factors, either activators or repressors to the control elements of the enhancers. The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.

34. What determines how much of a gene product will be produced? The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.

35. Promoter Enhancer Albumin gene Control elements Crystallin gene Liver cell nucleus Lens cell nucleus Available activators Available activators Albumin gene not expressed Albumin gene expressed Crystallin gene not expressed Crystallin gene expressed Lens cell Liver cell (b) (a) Combinatorial Control of Gene Activation • A particular combination of control elements • Will be able to activate transcription only when the appropriate activator proteins are present Figure 19.7a, b

36. Types of Genes Associated with Cancer

37. Cancer results from genetic changes that affect cell cycle control

38. What types of things influence having cancer? Mutations of genes associated with cell growth such as: random mutation, chemical carcinogens, X-rays, and some viruses.

39. Types of Genes Associated with Cancer Oncogenes Proto-oncogenes Tumor-Suppressor Genes

40. Oncogenes & Proto-Oncogenes Cancer causing genes Genes that stimulate normal cell growth & division • Converting Proto-Oncogenes into Oncogenes May promote excessive cell division and cancer

41. Tumor-Suppressor Genes • These genes encode proteins that prevent uncontrolled cell growth. • Repair damaged DNA • Control the adhesion of cells to each other or to the extracellular matrix • Components of cell signaling pathways that inhibit the cell cycle. • A mutation happens here and cells will divide uncontrollably = cancer.

42. Cell cycle – stimulating pathway

43. Cell cycle – inhibiting pathway

44. Mutations that knock out the p53 gene • Can lead to excessive cell growth and cancer (c) Effects of mutations. Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated, as in (a), or not inhibited when it normally would be, as in (b). EFFECTS OF MUTATIONS Protein overexpressed Protein absent Cell cycle not inhibited Cell cycle overstimulated Increased cell division Figure 19.12c

45. Multiple steps for the development of cancer. More than one somatic mutation is needed to produce full-fledged cancer cells. (the older we get the more likely we are to develop cancer) At least: 1 active oncogene and mutation or loss of several tumor-suppressor genes are recessive so both alleles must be “knocked out”

46. And finally…the telomerase gene is usually activated in many tumors Enzyme prevents DNA from shortening and when activated removes a natural limit on the number of times a cell can divide

47. Genetic Predisposition & other Factors Contributing to Cancer

48. Risk Factors • Inheriting an oncogene puts you one step closer to accumulating the mutations for cancer. • Breast cancer: a person inheriting one mutant BRCA1 allele has a 60% probability of developing cancer before the age of 50 compared to someone homozygous for normal (2%). • DNA breakage • Minimize exposure to these agents: • UV radiation, chemicals from cigarette smoke, X-rays • Viruses • Viral integration; can contribute oncogene, alter tumor supressor genes, or convert proto-oncogenes to oncogenes.

49. Genetic Basis of Development

50. Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.