Ch. 18 Regulation of Gene Expression 1 Human genome has around 23,688 genes (Scientific American 2/2006) Essential Questions: How is transcription regulated? How are genes expressed? 2 Bacteria regulate transcription based on their environment 1. can adjust activity of enzymes already present Ex. enz 1 inhibited by final product 2. Adjust level of certain enz. ­regulate the genes that code for the enzyme 3 Operon model ­ the tryptophan example The five genes that code for the subunits of the enzymes are clustered together. 4 Grouping genes that are related is advantageous ­ only need one "switch" to turn them on or off "Switch" = the operator (segment of DNA) ­located within the promoter ­controls RNA polymerase's access to the genes operon = the operator, the promoter, and the genes they control ­trp operon is an example in E.coli 5 operon can be switched off by a repressor protein ­binds to operator and blocks attachment of RNA polymerase to the promoter trp repressor is made from a regulatory gene called trpR 6 7 trpR has its own promoter regulatory genes are expressed continuously: ­binding of repressors to operators is reversible ­the trp repressor is an allosteric protein ­ has active and inactive shapes ­trp repressor is synthesized in inactive form 8 if tryptophan binds to trp repressor at an allosteric site, then becomes active and can attach to operator ­in this case tryptophan is a corepressor ­ a small molecule that cooperates with a repressor protein to switch operon off. 9 Two types of negative gene regulation: Repressible operons­ transcription is usually on, but is inhibited by the corepressor Ex. Trp operon Inducible operon ­ transcription is usually off, but can be stimulated by when a corepressor interacts with a regulatory protein Ex. lac operon 10 Example of an inducible operon: lac operon if lactose absent regulatory gene lacI, located outside operon codes for allosteric repressor protein that switches off lac operon 11 lac repressor is active by itself, binds to operator and switches lac operon off to turn lac operon on, need an inducer (allolactose) the inactivates the repressor the enzymes of the lac operon are inducible enzymes ­ synthesis is induced by a chemical signal ­usually function in catabolic pathways ­ break down nutrient repressible enzymes (ex. trp operon) usually function in anabolic pathways ­ make products 12 Positive gene regulation E. coli prefers glucose over lactose if both present ­when glucose is scarce ­ cyclic AMP (cAMP)a small organic molcule accumulates ­CAP (catabolite activator protein) is a regulatory protein ­ an activator ­ binds to DNA and stimulates transcription ­when cAMP binds to regulatory protein CAP becomes active shape and attaches upstream of lac promoter ­helps RNA polymerase bind 13 14 How is eukayotic gene expression regulated? All cells have the same genome (exception immune cells) ­only 20% of genes are expressed at any given time ­but get differentiated during development ­expression of the genes on the chromosomes is different for each differentiated cell = differential gene expression Ex. in a muscle cell a certain gene may be turned on in a skin cell, same gene may be turned off 15 Only 1.5% of DNA is coding DNA for proteins ­a small amount is used to make RNA ­rest is "noncoding" 16 control of gene expression in eukaryotic cells each stage represents a place where regulation can happen 17 Factors that affect transcription regulation: Chromatin structure: 1. if in heterochromatin ­ genes are not expressed 2. where promoter is in relation to nucleosomes and DNA 18 3. chemical modification to histones ­histone acetylation­ acetyl group attached to pos charged Lysine in histone tails ­if histone tails are acetylated, become neutral ­ no binding with other nucleosomes ­gives chromatin a looser structure ­transcription proteins have access to genes ­may be involved in transcription factors attaching to promoter site ­methylation to histone tails can lead to condensation of chromatin 19 4. DNA methylation ­to cytosine after DNA synthesis ­heavily methylated = genes not expressed Ex. inactivated X chromosome in mammals ­important for embryonic development to form specialized tissues 20 5. epigenetic inheritance ­ inheritance traits transmitted by mechanisms not involved in nucleotide sequence Ex. chromatin modifications that affect gene expression in future generations of cells 21 Regulation of transcription initiation: 6. chromatin modifying enzymes­ make DNA more or less able to bind to transcription complex 7. interactions between enhancers (control elements far upstream from promoter) and activators (protein that binds to an enhancer and stimulates transcription) 22 Eukaryotic gene and its transcript 23 1. Activator proteins bind to distal control elements (enhancer) 2. DNA bending protein brings activators closer to promoter 3. activators bind mediator proteins and transcription factors to form initation complex 24 8. Some transcription factors function as repressors ­ inhibit expression of a gene a. can block activators b. can bind to enhancer elements to turn off transcription even if activators are present 9. activators and repressors can influence chromatin structure ­some activators get proteins that acetylate histones near promoters to promote transcription ­some repressors get proteins to deacylate histones and reduce transcription = silencing 25 Eukaryotic organisms usually don't have operons like bacteria, however some genes are coexpressed ­found in clusters that have their own promoter and individually transcribed ­some are found on different chromosomes ­expression depends on a combination of elements that recognize control elements and bind to them, so all genes are transcribed at the same time 26 can be initiated by chemicals such as steroids (binds to an intracellular receptor protein) which then serves as a transcription activator ­nonsteroid signal molecules that don't enter cell but bind to surface, use signal transduction pathways 27 Mechanisms of post transcriptional regulation ­gene expression can be regulated at any post transcriptional step 1. RNA processing ­ Alternative RNA splicing ­ can produce different mRNA 28 2. mRNA degradation ­ ­prokaryotic mRNA degrades by enzymes in a few minutes ­eukaryotic mRNA survives, hours, days or weeks ­gets degraded by shortening poly­A tail and removal of 5' cap ­when cap removed nuclease enzymes can attack 29 3. Initiation of Translation can regulate genes ­during initiation stage ­regulatory proteins bind to specific sequences within the untranslated region of the 5' end (5' UTR) ­prevent ribosome attachment 30 4. Protein processing and degradation to control gene expression ­chemical modifications that make them functional ­need to be transported to particular places to function ­protein degradation ­ ubiquitin attaches to protein, proteasomes recognize the ubiquitin and degrade them 31 32 Noncoding RNAs can control gene expression ex. small RNAs occurs at two points: 1. mRNA translation 2. Chromatin configuration 33 MicroRNAs (miRNAs)= single stranded RNA ­formed from longer RNA precursors that fold back on themselves, forming short double­ stranded hairpin structures ­ held with hydrogen bonds ­dicer = enzyme that cuts RNA hairpin out ­one strand is degraded, other (miRNA)forms a complex with proteins ­can bind to mRNA with complementary sequence ­causes degration of mRNA or blocks translation 34 35 Remodeling Chromatin structure siRNAs = small interfering RNAs used in heterochromatin condensing 36 Regulation of gene expression during cell Differentiation determination = the events that lead to the observable differentiation of a cell ­once initiated ­ embryonic cell is "committed to its fate" ­happens in "tissue specifc proteins" ­ found only in a cell type and give the cell is structure and function 37 38 pattern formation­ spatial organization of tissues and organs ­in animals ­ begins in early embryo ­due to positional information provided by cytoplasmic determinants and inductive signals 39 Cancer Types of genes associated with cancer 1. tumor viruses­ transform cells through integration of viral nucleic acid into host cell Ex. Epstein Barr virus that causes mono has been linked to Burkett's lymphoma Papilloma virus linked to cervical cancer HTLV­1 (retrovirus) ­ causes adult leukemia 40 2. Oncogenes­cancer causing genes normal cellular genes = proto­oncogenes (code for proteins that stimulate cell growth and division) ­can become oncogenes via: a. movement of DNA within genome b. amplification of a proto­oncogene (more copies of a gene than normal) c. point mutations 1. within control element 2. within the gene 41 change of proto­onogenes into oncogenes 42 3. Tumor­suppressor genes­ ­code for proteins that normally inhibit cell division ­any mutation that decreases the activity of these genes can cause cancer 43 other functions of proteins made from these genes: 1. repair damaged DNA 2. control adhesion to cells to each other or to extracellular matrix­ anchorage to cells is important 44 3. regulate cell­signaling pathways that inhibit cell cycle a. ras gene = G protein that relays a signal from growth factor on membrane to protein kinases ­at end of pathway ­stimulates cell cycle ­will not operate unless correct amt. of growth factor ­mutation leads to hyperactive ras gene = increased cell division ­mutated in 30% of human cancers 45 Cell cycle ­ stimulating pathway 46 Cell cycle ­ inhibiting pathway 47 if cell cycle overstimulated or not inhibited 48 b. p53 gene­ codes for