1. Gene expression CHAPTER 18

2. Bacterial Gene Regulation  Bacteria regulate transcription based upon environmental conditions  E. coli depends on the eating habits of its host  If the host doesn’t eat foods with tryptophan-bacteria activates metabolic pathway  Produces tryptohan from another source  Gene regulation takes place via an operon  Key components  Operator – the switch that controls on/off  Promoter – the attachment site for RNA polymerase  Enzyme coding genes

3. Bacterial Gene Regulation  trp Operon  Is turned “on” in the absence of tryptophan  Is turned off by a repressor protein – trp repressor (trpR)  Blocks RNA polymerase from binding to the promoter  When tryptophan is present it binds to the repressor protein and blocks transcription  Prevents the enzymes that will synthesize tryptophan from other sources  This is called a repressible operon  Usually on but can be turned off by a particular molecule

4. Bacterial Gene Regulation  lac operon  Usually off, but turned on by the presence of a particular molecule  Β-galactosidase breaks down lactose into glucose and galactose  Without lactose, small amount of β- galactosidase produced  Genes for Β-galactosidase are located in the lac operon  Key componenets  lac I gene – regulatory gene that codes for a repressor  Inducer – small molecule that inactivates the repressor  This is called an inducible operon  The signal to start is induced by a molecule (lactose)

5. Bacterial Gene Regulation  Positive Gene Regulation  E.coli prefers glucose to lactose when both present  Only with metabolize lactose when glucose in short demand  cAMP (cyclic AMP) – accumulates when glucose is scarce  Involves an activator – protein that binds to DNA and causes transcription (catabolite activator protein)  As cAMP increases, it binds to CAP  This binds to promoter site upstream from lac promoter  Increases the affinity for RNA polymerase  As cAMP decreases (glucose increases) CAP detaches from promoter

6. Eukaryotic Gene Expression  Chromosome structure can affect gene expression  Modification to histone structure  Histone acetylation  Acetyl groups are attached to histone tails  Detach from neighboring nucleosomes  Easier for transcription proteins to access genes in aceltylated areas

7. Eukaryotic Gene Expression  Gene expression can be regulated by changing DNA  More or less affinity for transcription proteins (factors)  Can use Enhancers and Transcriptions factors  Enhancers can contain activators or repressors  Activator proteins bind to a distal control element in an enhancer  DNA bending protein brings the activators closer to the promoter  Activators bind to mediator proteins and transcription factors  Transcription initiation complex forms and transcription begins

8. Eukaryotic Gene Expression  Combinatorial control  All cells have the same DNA for coding  Differing control elements can control for gene expression in different cells  Turning genes on and off at the same time  Genes for enzymes of a metabolic pathway are typically on different chromosomes  Coordinated control usually occurs in response to external signals  Ex. Hormone entering a cell  Every gene in the pathway will respond to the signal  Some non-hormal signals bind to signal transduction pathways

9. Eukaryotic Gene Expression  New research has shown that DNA areas may loop into areas that are high in RNA polymerases in the nucleus  Chromosomes may interact with one another  Genes may also be relocated to transcription factories in the nucleus to ready for transcription

10. Eukaryotic Gene Expression  Transcription does not mean gene expression – amount of functional protein determines expression  Alternative RNA Spicing  Different mRNA molecules are produced from the same transcript  Can expand the number of genes available  mRNA Degradation  The amount of time mRNA is available can determine protein output  Initiation of Translation  Gene regulation can occur at the initiation of translation which can have an affect on gene expression  Protein Processing and Degradation  Proteins must be folded properly to function  Proteins have a designated amount of time they function within the cell before destruction

11. Eukaryotic Gene Expression  MicroRNA’s and Small Interfering RNA’s  miRNA’s – small single stranded RNA molecules  Long sequences that fold back on themselves  Form hairpin turns – cut away  Dicer cuts into short fragments  Forms a complex with proteins that can bind to mRNA  Either degrades the mRNA or blocks translation  siRNA’s – similar in function to miRNAs but have a longer strand

12. Cell Differentiation  What determines how the first cells will differentiate?  Egg cytoplasm contains RNA’s and proteins – cytoplasmic determinants  After the first division the two cells are exposed to different determinants  These determine which genes will be expressed in the cell  Cell environment – other major factor in embryonic gene expression  Induction – contact of cell to cell surface molecules  Binding of growth factors by neighboring cells

13. Cell Differentiation  Before development of organs, the body position must be determined  Cytoplasmic determinant and inductive signals contribute to spatial organization  Forms the axes of the body  Positional cues are cytoplasmic determinants and inductive signals – tell a cell its location relative to body axes and neighboring cells

14. Cell Differentiation  Homeotic genes (Hox genes)  In fruit flies, genes that control pattern formation late in embryo, larva, and adult development  Discovered by Edward B. Lewis by studying mutant fruit flies with abnormal patterns of development

15. Development of Cancer  The same systems important during development are prominent in cancer cells  Also have cancer causing genes – oncogenes  Normal genes are referred to as proto-oncogenes  Conversion to an oncogene – 3 ways:  Movement of DNA within the genome  Amplification of proto-oncogene  Point mutations in a control element of an proto- oncogene

16. Development of Cancer  Interference with cell signaling pathways  ras gene – proto-oncogene  Mutated in about 30% of human cancers  G-protein – relays a signal from a growth factor  Result is to stimulate the cell cycles  Mutations result in a hyperactive Ras protein in the absence of the growth factor – increased cell division  p53 gene – tumor suppressor gene  Mutated in 50% of human cancers  Called the guardian angel of the genome-activates many other genes  Codes for cell cycle inhibiting proteins  Leads to excessive cell growth

17. Development of Cancer  More than one somatic cell mutation is needed for production of a cancer cell  This is why cancer risk increases with age  Ex. Colorectal cancer  Starts as a normal benign polyp but divides frequently  May become malignant-also accumulates mutations converting proto- oncogenes to oncogenes and knocks out tumor suppressor genes  Cells become cancerous  About half a dozen changes needed at the DNA level for a cell to become cncersours

18. Development of Cancer  Inheritance of oncogenes or mutated tumor suppressor genes increases risk  5-10% breast cancer have a strong inheritance basis  Mutations to BRCA1 or BRCA2 are found in at least half inherited cancers  BRCA1 mutation has a 60% probability of developing breast cancer before age 50 (only 2% if no mutation)  BRCA genes are considered tumor suppressor genes  Both protein products function in DNA repair  Cancer can also be caused by viruses  Ex. Epstein-Barr virus (Lymphomas), Papillomaviruses (cervical cancer)  Viruses play a role in about 15% of all cancers