Honors Biology Reading Guide Chapter 11 v Promoter a specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins v Operator in prokaryotic DNA a sequence of nucleotides near the start of an operon to which an active repressor protein can attach the binding of a repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon the operator sequence thereby acts as a genetic switch that can turn all the genes in an operon on or off as a single functional unit v Operon a unit of genetic regulation common in prokaryotes a cluster of genes with related functions along with the promoter and operator that control their transcription v Repressor a protein that blocks the transcription of a gene or operon v Regulatory gene a gene that codes for a protein which as a repressor that controls the transcription of another gene or groups of genes v Gene expression controlled Ø Overall process genetic information gene to proteins Ø Makes possible for cells produces specific kinds of protein when and where they are needed v How do you change the environment in your intestines Ø Eating other foods/changing foods you eat v In e coli the default state of the gene is of how does this work Ø Hen no lactose in cells environment transcription turned off by repressor protein functions by binding to operator physically blocking the attachment of RNA polymerase to the promoter regulatory gene code for repressor and is expressed continually so cell always has supply repressor molecules Ø When on lactose interferes lac repressor to operator by binding to repressor and changing its shape = cant bind to operator = operator stays on v What happens when lactose is not in e coli environment Ø Not waste time making enzymes to absorb sugar Ø Also save energy
v What happens to lac operon when milk is present in e coli s environment Ø Makes enzymes necessary absorb the sugar and use energy source v What happens to the trp operon when tryptophan is present in e coli s environment Ø Tryptophan binds to the repressor of the trp operon activated trp repressor switch off operon allows bacteria stop making certain essential molecules already present environment save materials and energy of the cells v Trp operon when tryptophan is absent Ø Can make tryptophan from scratch using enzymes encoded in trp operon but will stop making tryptophan and absorb it in prefabricated form fro surroundings whenever possible v How do activators work Ø Proteins turn operons on by binding to DNA act by making it easier for RNA polymerase to bind to the promoter rather than by blocking RNA polymerase like repressors help control wide variety operons v Differentiation the specialization in the structure and function of cells that occurs during the development of an organism results from selective activation and activation of the cell genes v Nucleosome the bead like unit of DNA packing in eukaryotic cell consists of DNA wound around a protein core made up of eight histone molecules v Histone a small protein molecules associated with DNA and important in DNA packing in the eukaryotic chromosomes eukaryotic chromatin consists of roughly equal parts of DNA and histone protein v Epigenic inheritance the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome such as the chemical modification of histone proteins or DNA bases v Packing and unpacking of DNA Ø Pack histones attach to DNA double helix next beaded string wrapped into tight helical fiber, fiber coils further into thick supercoil looping and folding can further compact the DNA packing can block gene expression by preventing RNA polymerase and other transcription proteins contacting DNA Ø Cells seem to use higher levels of packing for long term inactivation of genes v Chemical modification Ø Help regulate gene expression for addition chemical groups to some amino acids in histone proteins or removal can cause proteins to being to DNA tighter/loosen altering transcription machinery reach those genes DNA itself can be target huge example methylation mechanism gene expression but improperly done can lead to problems v Epigenic inheritance Ø The inheritance of traits transmitted by mechanisms not directly involving nucleotide sequence of a genome such as the chemical modification of histone proteins or DNA bases Ø Barr body A dense body formed from a deactivated X chromosomes found in the nuclei of female mammalian cells Ø X chromosome inactivation
In female mammals the inactivation of one X chromosome in each somatic cell initiated early embryotic development Ø Example Which X chromosome inactivated matter of change but once X chromosome inactivated all descendants cell have same copy turned off Tortoise shell cat v Transcription factors in the eukaryotic cell of a protein that functions in initiating or regulating transcription, transcription factors bind to DNA of the other proteins that bind to DNA v Enhancers a eukaryotic DNA sequence that helps stimulate the transcription of a gene at some distance from it on enhancer functions by means of a transcription gene at some distance from it an enhancer functions by means of a transcription factor called an activator which binds to it and then to the rest of the transcription apparatus v Silencers a eukaryotic DNA sequence that functions to inhibit the start of gene transcription may act analogously to an enhancer by binding a repressor v Activators a protein that switched on a gene or group of genes v How eukaryotic cell controls the expression of the gene Ø Pack/unpack DNA (chromosomal) proceeds coarse adjustment eukaryotic gene expression making region DNA more/less available transcription begins transcription have activators and repressors bind specific segments DNA promote or block binding RNA polymerase transcription genes on/off most
eukaryotic genes have individual promoters and other control sequences not clustered together operons v How important are activators compared to repressors in eukaryotic cells Ø More important v What is the default state for most specialized cells (eukaryotic) Ø Multicellular eukaryotes default stage off typical plant/animal cell needs to turn on small percentages genes required for cells specialized structure and function v What is the default state of genes translated into proteins used in routine cell function like glycolysis Ø House keeping genes continually active virtually all cells for routine activities such as glycolysis may be in an on state by default v What eukaryotic cells need to turn on genes of related functions like those of a metabolic pathways those genes may be scattered across different chromosomes since eukaryotic cells do not have operons like prokaryotic cells how do they make sure all of the needed genes are turned on for transcription Ø Association of specific combination of control sequences with every gene of a particularly metabolic pathway copies of the activators that recognize these control sequences bind to them all at once (once they are all identical) promoting stimulus transcription of the genes no matter where they are in the genome v Alternate RNA splicing Ø A type of regulation at the RNA processing level in which different mrna molecules are produced from the same primary transcript depending on which RNA segments are treated as exons and which as introns Ø Fruit fly differences males and females largely due to different patterns of RNA splicing Ø Results human genome project suggest that alternate splicing is very common in humans One gene shoes transcript an be sliced to encode 7 different versions of a protein each of which is made in a different type of cell v How much of the human genome codes from proteins Ø 1.5% v How much of the human genome does for rrna or trna Ø Very small portion v Is the rest of DNA lacking genome information Ø Significant amount genome is transcribed into functioning but non- protein coding RNAs including variety small RNAs v What are small RNA molecules called Ø MicroRNAs (mirna) v What can they bind to Ø Complementary sequences mrna molecules v What tis their function Ø Forms a complex with protein mrna protein complex can bind to any mrna molecule with the complementary sequence than the complexes then degraded the target mrna or blocks its translation
v How do researchers use mirna Ø Artificially control gene expression v How much of the expression of the human genome do they regulate Ø 1/3 all human genes v What is the use of mirna called Ø RNA interference (RNAi) v Important discovery relating to mirna Ø Particular mirna essential proper functioning pancreas without it inulin producing beta cells dies off can lead to diabetes v Breakdown of mrna Ø Molecules mrna not intact forever enzymes in cytoplasm break them down timing this event important factor regulating amounts proteins produced in cell longer mrna can be translated many times protein molecules then short lived ones v Difference in mrna breakdown in prokaryotes vs. eukaryotes Ø Eukaryotes Hors/week lifetime Ø Prokaryotes Short lifetime Degraded enzymes within few minutes synthesis (bacteria change protein production so quickly response environmental changes) v Initiation of translation Ø Among molecules involved in translation are the great many proteins that control the start of polypeptide synthesis by controlling the start of protein synthesis cells can avoid wasting energy if the needed components are currently unavailable v Protein activation Ø After translation some peptides require alteration to become functional post translation control mechanisms in eukaryotes often involved cutting of a polypeptide to yield a smaller final product that is the active protein able to carry out a specific function in the organism v Protein breakdown Ø Some proteins that trigger metabolic changes in cells are broken down within a few minutes or hours time regulation allows a cell to adjust the kinds and mounts of proteins in response to changes in the environment enables cells to maintains its proteins in prime working order v Homeotic genes Ø A master controlled gene that determined the identity of a body structure of a developing organism presumably by controlling the developmental rate of a group of cells
v Steps Ø Signaling cells secretes a signaling molecules Ø This molecule binds to the receptor protein embedded I the target cells plasma membrane Ø The binding activates the first in a series of relay proteins within the target cell each relay molecule activates another Ø The last relay molecules in the series activates a transcription factor that Ø Triggers transcription of a specific gene Ø Translation of the mrna procures a protein v Difference embryonic and adult stem cells Ø Embryonic More promising for medical applications Cells in the early animal embryo differentiate to give rise to all the cell types in the body In labs can divide indefinitely Right conditions can induce changes in gene expressions cause differentiations into a variety of cells Ø Adults Serve replace non- reproducing cells Give rise to many but not all cell types in organism Tiny number of stem cells v Oncogene a cancer causing genre usually contributes to malignancy by abnormally enhancing the amount of activity of a growth factor made by the cell v Proto- oncogene Ø Abnormal gene that through mutation can be converted to a cancer causing gene Ø Tumor- suppressing genes a genes whose product inhibits cell division thereby preventing uncontrolled cell growth a mutation that deactivates a tumor suppressor gene may lead to cancer v How might a proto- oncogene a gene that has an essential function in normal cells become and oncogene, a cancer causing gene Ø In general an oncogene arises from a genetic change that leads to an increase either in the amount of the proto- oncogenes protein product of the activity of each protein molecule Ø Normal gene expression changed cell stimulate to divide excessively