How Genes are Controlled

1. How Genes are Controlled CM Lamberty General Biology

2. Tobacco’s Smoking Gun • Southern US major tobacco producer • 1950’s: ½ of all Americans smoked 1+ packs/day • “health benefits” • Rate of lung cancer increased in proportion to tobacco use • 1990: lung cancer killing over twice as many men as any other type of cancer • 1996: direct link b/t tobacco and cancer • BPDE from tobacco smoke binds to DNA w/ gene p53 which codes for protein that normally suppresses tumors

3. How and Why Genes are Regulated • Every somatic cell is produced by repeated rounds of mitosis starting from zygote • Each cell has same DNA as zygote • Every somatic cell contains every gene. • How do cells become different? • Contol mechanisms turn on certain genes and turn others off • Cellular differentiation • Specialized in structure and function • Gene regulation • The turning on or off of genes

4. Patterns of Gene Expression • In gene expression • A gene is turned on and transcribed into RNA • Information flows from • Genes to proteins • Genotype to phenotype • Information flows from DNA to RNA to proteins. • The great differences among cells in an organism must result from the selective expression of genes.

6. Gene Regulation in Bacteria • Natural selection has favored bacteria that express • Only certain genes • Only at specific times when the products are needed by the cell • So how do bacteria selectively turn their genes on and off? • An operon includes • A cluster of genes with related functions • The control sequences that turn the genes on or off • The bacterium E. coli used the lac operon to coordinate the expression of genes that produce enzymes used to break down lactose in the bacterium’s environment. • The lac operon uses • A promoter, a control sequence where the transcription enzyme initiates transcription • An operator, a DNA segment that acts as a switch that is turned on or off • A repressor, which binds to the operator and physically blocks the attachment of RNA polymerase

8. Gene Regulation in Eukaryotic Cells • Eukaryotic cells have more complex gene regulating mechanisms with many points where the process can be regulated, as illustrated by this analogy to a water supply system with many control valves along the way.

9. Chromosome Unpacking of DNA DNA Gene Figure 11.3-1

10. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Figure 11.3-2

11. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Nucleus Cap Tail mRNA in nucleus Cytoplasm mRNA in cytoplasm Figure 11.3-3

12. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Nucleus Cap Tail mRNA in nucleus Cytoplasm mRNA in cytoplasm Breakdown of mRNA Figure 11.3-4

13. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Nucleus Cap Tail mRNA in nucleus Cytoplasm mRNA in cytoplasm Breakdown of mRNA Translation of mRNA Polypeptide Figure 11.3-5

14. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Nucleus Cap Tail mRNA in nucleus Cytoplasm mRNA in cytoplasm Breakdown of mRNA Translation of mRNA Polypeptide Various changes to polypeptide Active protein Figure 11.3-6

15. Chromosome Unpacking of DNA DNA Gene Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Nucleus Cap Tail mRNA in nucleus Cytoplasm mRNA in cytoplasm Breakdown of mRNA Translation of mRNA Polypeptide Various changes to polypeptide Active protein Breakdown of protein Figure 11.3-7

16. Gene Regulation in Eukaryotic Cells • The Regulation of DNA packing • Cells may use DNA packing for long-term inactivation of genes • X chromosome inactivation • Occurs in female mammals • Is when one of the two X chromosomes in each cell is inactivated at random • All of the descendants will have the same X chromosome turned off. • If a female cat is heterozygous for a gene on the X chromosome • About half her cells will express one allele • The others will express the alternate allele

17. Two cell populations in adult cat: Early embryo: Active X Orange fur Inactive X Cell division and X chromosome inactivation X chromosomes Allele for black fur Allele for orange fur Inactive X Black fur Active X Figure 11.4

18. Gene Regulation in Eukaryotic Cells • The Initiation of Transcription • The initiation of transcription is the most important stage for regulating gene expression. • In prokaryotes and eukaryotes, regulatory proteins • Bind to DNA • Turn the transcription of genes on and off • Unlike prokaryotic genes, transcription in eukaryotes is complex, involving many proteins, called transcription factors, that bind to DNA sequences called enhancers. • Repressor proteins called silencers • Bind to DNA • Inhibit the start of transcription • Activators are • More typically used by eukaryotes • Turn genes on by binding to DNA

19. Enhancers (DNA control sequences) RNA polymerase Bend in the DNA Transcription Gene Promoter Transcription factor Figure 11.5

20. Gene Regulation in Eukaryotic Cells • RNA Processing and Breakdown • The eukaryotic cell • Localizes transcription in the nucleus • Processes RNA in the nucleus • RNA processing includes the • Addition of a cap and tail to the RNA • Removal of any introns • Splicing together of the remaining exons • In alternative RNA splicing, exons may be spliced together in different combinations, producing more than one type of polypeptide from a single gene. • Eukaryotic mRNAs • Can last for hours to weeks to months • Are all eventually broken down and their parts recycled • Small single-stranded RNA molecules, called microRNAs (miRNAs), bind to complementary sequences on mRNA molecules in the cytoplasm, and some trigger the breakdown of their target mRNA.

21. Exons 4 1 2 3 5 DNA Figure 11.6-1

22. Exons 4 1 2 3 5 DNA 4 3 5 2 1 RNA transcript Figure 11.6-2

23. Exons 4 1 2 3 5 DNA 4 3 5 2 1 RNA transcript RNA splicing or 1 1 2 2 mRNA 3 4 5 5 Figure 11.6-3

24. Gene Regulation in Eukaryotic Cells • The Initiation of Translation • The process of translation offers additional opportunities for regulation. • Protein Activation and Breakdown • Post-translational control mechanism • Occur after translation • Often involve cutting polypeptides into smaller, active final products • The selective breakdown of proteins is another control mechanism operating after translation.

26. Cell Signaling • In a multicellular organism, gene regulation can cross cell boundaries. • A cell can produce and secrete chemicals, such as hormones, that affect gene regulation in another cell. • Homeotic Genes

27. SIGNALING CELL Secretion Signal molecule Plasma membrane TARGET CELL Nucleus Figure 11.8-1

28. SIGNALING CELL Secretion Signal molecule Plasma membrane Reception Receptor protein TARGET CELL Nucleus Figure 11.8-2

29. SIGNALING CELL Secretion Signal molecule Plasma membrane Reception Receptor protein TARGET CELL Signal transduction pathway Nucleus Figure 11.8-3

30. SIGNALING CELL Secretion Signal molecule Plasma membrane Reception Receptor protein TARGET CELL Signal transduction pathway Transcription factor (activated) Nucleus Figure 11.8-4

31. SIGNALING CELL Secretion Signal molecule Plasma membrane Reception Receptor protein TARGET CELL Signal transduction pathway Transcription factor (activated) Nucleus Response Transcription mRNA Figure 11.8-5

32. SIGNALING CELL Secretion Signal molecule Plasma membrane Reception Receptor protein TARGET CELL Signal transduction pathway Transcription factor (activated) Nucleus Response Transcription mRNA New protein Translation Figure 11.8-6

33. Homeotic Genes • Master control genes that regulate groups of other genes that determine what body parts will develop in which locations • Mutations can produce bizarre effects • Similar homeotic genes help direct embryonic development in nearly every eukaryotic organism.

35. DNA Microarrays • A DNA microarray allows visualization of gene expression. • The pattern of glowing spots enables the researcher to determine which genes were being transcribed in the starting cells. • Researchers can thus learn which genes are active in different tissues or in tissues from individuals in different states of health.

36. mRNA isolated Figure 11.11-1

37. mRNA isolated Reverse transcriptase and fluorescently labeled DNA nucleotides Fluorescent cDNA cDNA made from mRNA Figure 11.11-2

38. mRNA isolated Reverse transcriptase and fluorescently labeled DNA nucleotides Fluorescent cDNA cDNA made from mRNA DNA microarray cDNA mixture added to wells Figure 11.11-3

39. mRNA isolated Reverse transcriptase and fluorescently labeled DNA nucleotides Fluorescent cDNA cDNA made from mRNA DNA microarray cDNA mixture added to wells Unbound cDNA rinsed away Nonfluorescent spot Fluorescent spot Fluorescent cDNA DNA microarray (6,400 genes) DNA of an expressed gene DNA of an unexpressed gene Figure 11.11-4

40. Cloning Plants and Animals • The Genetic Potential of Cells • Differentiated cells • All contain a complete genome • Have the potential to express all of an organism’s genes • Differentiated plant cells can develop into a whole new organism. • The somatic cells of a single plant can be used to produce hundreds of thousands of clones. • Plant cloning • Demonstrates that cell differentiation in plants does not cause irreversible changes in the DNA • Is now used extensively in agriculture

42. The Genetic Potential of Cells • Regeneration • Is the regrowth of lost body parts • Occurs, for example, in the regrowth of the legs of salamanders

43. Reproductive Cloning of Animals • Nuclear transplantation • Involves replacing nuclei egg cells with nuclei from differentiated cells • Has been used to clone a variety of animals • In 1997, Scottish researchers produced Dolly, a sheep, by replacing the nucleus of an egg cell with the nucleus of an adult somatic cell in a procedure called reproductive cloning, because it results in the birth of a new animal.

45. Practical Applications of Reproductive cloning • Other mammals have since been produced using this technique including • Farm animals • Control animals for experiments • Rare animals in danger of extinction

47. Human Cloning • Cloning of animals • Has heightened speculation about human cloning • Is very difficult and inefficient. • Critics raise practical and ethical objections to human cloning

48. Therapeutic Cloning and Stem Cells • The purpose of therapeutic cloning is not to produce viable organisms but to produce embryonic stem cells • Embryonic stem cells (ES cells) • Are derived from blastocyst • Can give rise to specific types of differentiated cells • Adult Stem Cells • Are cells in adult tissue • Generate replacements for nondividing differentiated cells • Embryonic vs. Adult Stem cells • Adult cells are partway along the road to differentiation • Usually give rise to only a few related types of specialized cells.

50. Umbilical Cord Blood Banking • Umbilical Cord Blood • Can be collected at birth • Contains partially differentiated stem cells • Has had limited success in the treatment of a few diseases American Association of Pediatrics recommends cord blood banking only for babies born into a family with know genetic risk