DOCSLIB.ORG

Ch. 18 Regulation of Gene Expression

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

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
Recommended publications
  • Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for Cellular Control and Differentiation

    Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for Cellular Control and Differentiation

    Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for cellular control and differentiation. • Understanding “expression” is a “hot” area in Biology. General Mechanisms 1. Regulate Gene Expression 2. Regulate Protein Activity Operon Model • Jacob and Monod (1961) - Prokaryotic model of gene control. • Always on the National AP Biology exam! Operon Structure 1. Regulatory Gene 2. Operon Area a. Promoter b. Operator c. Structural Genes Gene Structures Regulatory Gene • Makes Repressor Protein which may bind to the operator. • Repressor protein blocks transcription. Promoter • Attachment sequence on the DNA for RNA polymerase to start transcription. Operator • The "Switch”, binding site for Repressor Protein. • If blocked, will not permit RNA polymerase to pass, preventing transcription. Structural Genes • Make the enzymes for the metabolic pathway. Lac Operon • For digesting Lactose. • Inducible Operon - only works (on) when the substrate (lactose) is present. If no Lactose • Repressor binds to operator. • Operon is "off”, no transcription, no enzymes made If Lactose is absent If Lactose is present • Repressor binds to Lactose instead of operator. • Operon is "on”, transcription occurs, enzymes are made. If Lactose is present Enzymes • Digest Lactose. • When enough Lactose is digested, the Repressor can bind to the operator and switch the Operon "off”. Net Result • The cell only makes the Lactose digestive enzymes when the substrate is present, saving time and energy. Animation • http://www.biostudio.com/d_%20Lac%20Ope ron.htm trp Operon • Makes/synthesizes Tryptophan. • Repressible Operon. – Predict how it is different from the inducible operon… If no Tryptophan • Repressor protein is inactive, Operon "on” Tryptophan made. • “Normal” state for the cell.
  • Original Article EP300 Regulates the Expression of Human Survivin Gene in Esophageal Squamous Cell Carcinoma

    Original Article EP300 Regulates the Expression of Human Survivin Gene in Esophageal Squamous Cell Carcinoma

    Int J Clin Exp Med 2016;9(6):10452-10460 www.ijcem.com /ISSN:1940-5901/IJCEM0023383 Original Article EP300 regulates the expression of human survivin gene in esophageal squamous cell carcinoma Xiaoya Yang, Zhu Li, Yintu Ma, Xuhua Yang, Jun Gao, Surui Liu, Gengyin Wang Department of Blood Transfusion, The Bethune International Peace Hospital of China PLA, Shijiazhuang 050082, Hebei, P. R. China Received January 6, 2016; Accepted March 21, 2016; Epub June 15, 2016; Published June 30, 2016 Abstract: Survivin is selectively up-regulated in various cancers including esophageal squamous cell carcinoma (ESCC). The underlying mechanism of survivin overexpression in cancers is needed to be further studied. In this study, we investigated the effect of EP300, a well known transcriptional coactivator, on survivin gene expression in human esophageal squamous cancer cell lines. We found that overexpression of EP300 was associated with strong repression of survivin expression at the mRNA and protein levels. Knockdown of EP300 increased the survivin ex- pression as indicated by western blotting and RT-PCR analysis. Furthermore, our results indicated that transcription- al repression mediated by EP300 regulates survivin expression levels via regulating the survivin promoter activity. Chromatin immunoprecipitation (ChIP) analysis revealed that EP300 was associated with survivin gene promoter. When EP300 was added to esophageal squamous cancer cells, increased EP300 association was observed at the survivin promoter. But the acetylation level of histone H3 at survivin promoter didn’t change after RNAi-depletion of endogenous EP300 or after overexpression of EP300. These findings establish a negative regulatory role for EP300 in survivin expression. Keywords: Survivin, EP300, transcription regulation, ESCC Introduction transcription factors and the basal transcrip- tion machinery, or by providing a scaffold for Survivin belongs to the inhibitor of apoptosis integrating a variety of different proteins [6].
  • RNA-Based Regulation of Genes of Tryptophan Synthesis and Degradation, in Bacteria

    RNA-Based Regulation of Genes of Tryptophan Synthesis and Degradation, in Bacteria

    REVIEW RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria CHARLES YANOFSKY Department of Biological Sciences, Stanford University Stanford, California 94305, USA ABSTRACT We are now aware that RNA-based regulatory mechanisms are commonly used to control gene expression in many organisms. These mechanisms offer the opportunity to exploit relatively short, unique RNA sequences, in altering transcription, translation, and/or mRNA stability, in response to the presence of a small or large signal molecule. The ability of an RNA segment to fold and form alternative hairpin secondary structures—each dedicated to a different regulatory function—permits selection of specific sequences that can affect transcription and/or translation. In the present paper I will focus on our current understanding of the RNA-based regulatory mechanisms used by Escherichia coli and Bacillus subtilis in controlling expression of the tryptophan biosynthetic operon. The regulatory mechanisms they use for this purpose differ, suggesting that these organisms, or their ancestors, adopted different strategies during their evolution. I will also describe the RNA-based mechanism used by E. coli in regulating expression of its operon responsible for tryptophan degradation, the tryptophanase operon. Keywords: trp operon; trp suboperon; aro supraoperon; tna operon; transcription attenuation; T box regulation; tryptophan as a regulatory signal; tRNATrp as a regulatory signal; peptidyl-tRNA; ribosome mediated regulation INTRODUCTION A second regulatory lesson learned over the years is that information within mRNAs, or other RNAs, as well as small Studies over the past 50+ years have revealed that metabolites and other molecules—in addition to DNA and optimization of gene expression has been a major evolu- proteins—often provides specific regulatory signals, or tionary objective for most species.
  • Molecular and Cellular Signaling

    Molecular and Cellular Signaling

    Martin Beckerman Molecular and Cellular Signaling With 227 Figures AIP PRESS 4(2) Springer Contents Series Preface Preface vii Guide to Acronyms xxv 1. Introduction 1 1.1 Prokaryotes and Eukaryotes 1 1.2 The Cytoskeleton and Extracellular Matrix 2 1.3 Core Cellular Functions in Organelles 3 1.4 Metabolic Processes in Mitochondria and Chloroplasts 4 1.5 Cellular DNA to Chromatin 5 1.6 Protein Activities in the Endoplasmic Reticulum and Golgi Apparatus 6 1.7 Digestion and Recycling of Macromolecules 8 1.8 Genomes of Bacteria Reveal Importance of Signaling 9 1.9 Organization and Signaling of Eukaryotic Cell 10 1.10 Fixed Infrastructure and the Control Layer 12 1.11 Eukaryotic Gene and Protein Regulation 13 1.12 Signaling Malfunction Central to Human Disease 15 1.13 Organization of Text 16 2. The Control Layer 21 2.1 Eukaryotic Chromosomes Are Built from Nucleosomes 22 2.2 The Highly Organized Interphase Nucleus 23 2.3 Covalent Bonds Define the Primary Structure of a Protein 26 2.4 Hydrogen Bonds Shape the Secondary Structure . 27 2.5 Structural Motifs and Domain Folds: Semi-Independent Protein Modules 29 xi xü Contents 2.6 Arrangement of Protein Secondary Structure Elements and Chain Topology 29 2.7 Tertiary Structure of a Protein: Motifs and Domains 30 2.8 Quaternary Structure: The Arrangement of Subunits 32 2.9 Many Signaling Proteins Undergo Covalent Modifications 33 2.10 Anchors Enable Proteins to Attach to Membranes 34 2.11 Glycosylation Produces Mature Glycoproteins 36 2.12 Proteolytic Processing Is Widely Used in Signaling 36 2.13 Reversible Addition and Removal of Phosphoryl Groups 37 2.14 Reversible Addition and Removal of Methyl and Acetyl Groups 38 2.15 Reversible Addition and Removal of SUMO Groups 39 2.16 Post-Translational Modifications to Histones .
  • Chapter 3. the Beginnings of Genomic Biology – Molecular

    Chapter 3. the Beginnings of Genomic Biology – Molecular

    Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1.
  • Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the Tna Operon of Escherichia Coli

    Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the Tna Operon of Escherichia Coli

    JOURNAL OF BACTERIOLOGY, Aug. 1995, p. 4451–4456 Vol. 177, No. 15 0021-9193/95/$04.0010 Copyright 1995, American Society for Microbiology Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the tna Operon of Escherichia coli CHARLES YANOFSKY* AND VIRGINIA HORN Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Received 13 March 1995/Accepted 27 May 1995 The growth-inhibiting drug bicyclomycin, known to be an inhibitor of Rho factor activity in Escherichia coli, was shown to increase basal level expression of the tryptophanase (tna) operon and to allow growth of a tryptophan auxotroph on indole. The drug also relieved polarity in the trp operon and permitted growth of a trp double nonsense mutant on indole. Nine bicyclomycin-resistant mutants were isolated and partially characterized. Recombination data and genetic and biochemical complementation analyses suggest that five have mutations that affect rho, three have mutations that affect rpoB, and one has a mutation that affects a third locus, near rpoB. Individual mutants showed decreased, normal, or increased basal-level expression of the tna operon. All but one of the resistant mutants displayed greatly increased tna operon expression when grown in the presence of bicyclomycin. The tna operon of the wild-type drug-sensitive parent was also shown to be highly expressed during growth with noninhibitory concentrations of bicyclomycin. These findings demonstrate that resistance to this drug may be acquired by mutations at any one of three loci, two of which appear to be rho and rpoB. Zwiefka et al. (24) found that the antibiotic bicyclomycin segment and interacts with the transcribing RNA polymerase (bicozamycin), an inhibitor of the growth of several gram- molecule, causing it to terminate transcription (7, 9).
  • GENE REGULATION Differences Between Prokaryotes & Eukaryotes

    GENE REGULATION Differences Between Prokaryotes & Eukaryotes

    GENE REGULATION Differences between prokaryotes & eukaryotes Gene function Description of Prokaryotic Chromosome and E.coli Review Differences between Prokaryotic & Eukaryotic Chromosomes Four differences Eukaryotic Chromosomes Form Length in single human chromosome Length in single diploid cell Proteins beside histones Proportion of DNA that codes for protein in prokaryotes eukaryotes humans Regulation of Gene Expression in Prokaryotes Terms promoter structural gene operator operon regulator repressor corepressor inducer The lac operon - Background E.coli behavior presence of lactose and absence of lactose behavior of mutants outcome of mutants The Lac operon Regulates production of b-galactosidase http://www.sumanasinc.com/webcontent/animations/content/lacoperon.html The trp operon Regulates the production of the enzyme for tryptophan synthesis http://bcs.whfreeman.com/thelifewire/content/chp13/1302002.html General Summary During transcription, RNA remains briefly bound to the DNA template Structural genes coding for polypeptides with related functions often occur in sequence Two kinds of regulatory control positive & negative General Summary Regulatory efficiency is increased because mRNA is translated into protein immediately and broken down rapidly. 75 different operons comprising 260 structural genes in E.coli Gene Regulation in Eukaryotes some regulation occurs because as little as one % of DNA is expressed Gene Expression and Differentiation Characteristic proteins are produced at different stages of differentiation producing cells with their own characteristic structure and function. Therefore not all genes are expressed at the same time As differentiation proceeds, some genes are permanently “turned” off. Example - different types of hemoglobin are produced during development and in adults. DNA is expressed at a precise time and sequence in time.
  • What Makes the Lac-Pathway Switch: Identifying the Fluctuations That Trigger Phenotype Switching in Gene Regulatory Systems

    What Makes the Lac-Pathway Switch: Identifying the Fluctuations That Trigger Phenotype Switching in Gene Regulatory Systems

    What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems Prasanna M. Bhogale1y, Robin A. Sorg2y, Jan-Willem Veening2∗, Johannes Berg1∗ 1University of Cologne, Institute for Theoretical Physics, Z¨ulpicherStraße 77, 50937 K¨oln,Germany 2Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands y these authors contributed equally ∗ correspondence to [email protected] and [email protected]. Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria, fate selection in viral infection, cell cycle control, and development. Stochastic switching between different phenotypes can occur as the result of random fluctuations in molecular copy numbers of mRNA and proteins arising in transcription, translation, transport, and binding. However, which component of a pathway triggers such a transition is gen- erally not known. By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply this method to the transition between the uninduced and induced states of the lac genes. We find that the transition to the induced state is not caused only by the single event of lac-repressor unbinding, but depends crucially on the time period over which the repressor remains unbound from the lac-operon. We confirm this notion in strains with a high expression level of the repressor (leading to shorter periods over which the lac-operon remains un- bound), which show a reduced switching rate.
  • I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB

    I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB

    BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac B M B 400 Part Four: Gene Regulation Section I = Chapter 15 POSITIVE AND NEGATIVE CONTROL SHOWN BY THE lac OPERON OF E. COLI A. Definitions and general comments 1. Operons An operon is a cluster of coordinately regulated genes. It includes structural genes (generally encoding enzymes), regulatory genes (encoding, e.g. activators or repressors) and regulatory sites (such as promoters and operators). 2. Negative versus positive control a. The type of control is defined by the response of the operon when no regulatory protein is present. b. In the case of negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated. c. In the case of positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Table 4.1.1. Positive vs. negative control BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac 3. Catabolic versus biosynthetic operons a. Catabolic pathways catalyze the breakdown of nutrients (the substrate for the pathway) to generate energy, or more precisely ATP, the energy currency of the cell. In the absence of the substrate, there is no reason for the catabolic enzymes to be present, and the operon encoding them is repressed. In the presence of the substrate, when the enzymes are needed, the operon is induced or de-repressed.
  • Teaching Gene Regulation in the High School Classroom, AP Biology, Stefanie H

    Teaching Gene Regulation in the High School Classroom, AP Biology, Stefanie H

    Wofford College Digital Commons @ Wofford Arthur Vining Davis High Impact Fellows Projects High Impact Curriculum Fellows 4-30-2014 Teaching Gene Regulation in the High School Classroom, AP Biology, Stefanie H. Baker Wofford College, [email protected] Marie Fox Broome High School Leigh Smith Wofford College Follow this and additional works at: http://digitalcommons.wofford.edu/avdproject Part of the Biology Commons, and the Genetics Commons Recommended Citation Baker, Stefanie H.; Fox, Marie; and Smith, Leigh, "Teaching Gene Regulation in the High School Classroom, AP Biology," (2014). Arthur Vining Davis High Impact Fellows Projects. Paper 22. http://digitalcommons.wofford.edu/avdproject/22 This Article is brought to you for free and open access by the High Impact Curriculum Fellows at Digital Commons @ Wofford. It has been accepted for inclusion in Arthur Vining Davis High Impact Fellows Projects by an authorized administrator of Digital Commons @ Wofford. For more information, please contact [email protected]. High Impact Fellows Project Overview Project Title, Course Name, Grade Level Teaching Gene Regulation in the High School Classroom, AP Biology, Grades 9-12 Team Members Student: Leigh Smith High School Teacher: Marie Fox School: Broome High School Wofford Faculty: Dr. Stefanie Baker Department: Biology Brief Description of Project This project sought to enhance high school students’ understanding of gene regulation as taught in an Advanced Placement Biology course. We accomplished this by designing and implementing a lab module that included a pre-lab assessment, a hands-on classroom experiment, and a post-lab assessment in the form of a lab poster. Students developed lab skills while simultaneously learning about course content.
  • Binds Multiple Sites Within the Aroh and Trp Operators

    Binds Multiple Sites Within the Aroh and Trp Operators

    Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Escherichia cod tryptophan repressor binds multiple sites within the aroH and trp operators Andrew A. Kumamoto, ~ William G. Miller, 2 and Robert P. GunsalusL2 1Molecular Biology Institute and the 2Department of Microbiology, University of Califomia, Los Angeles, Califomia 90024 USA DNase I footprinting and methylation protection studies have been used to analyze the binding of Escherichia coli Trp repressor to the trpR, aroH, and trp operators. The methylation protection assay shows that Trp repressor binds in two successive major grooves of the trpR operator, three successive major grooves of the aroH operator, and four successive major grooves of the trp operator. The simplest model that explains the difference in Trp repressor interaction at the three operators is that the aroH and trp operators are composed of multiple, helically stacked binding sites. When viewed in three dimensions, each site is positioned on a different face of the DNA, and together process up the surface of the DNA helix. Analysis of a deletion derivative of the trp operator supports this model. [Key Words" Trp repressor; aroH operator; trp operator; repressor binding] Received February 23, 1987; revised version accepted June 6, 1987. The Trp repressor of Escherichia coli coordinately regu- and by the isolation of constitutive mutations within lates the expression of the trp, aroH, and trpR operons in the trp operator {Bennett and Yanofsky 1978). These op- response to the intracellular levels of L-tryptophan erator constitutive mutations map at positions -16, (Cohen and Jacob 1959; Brown 1968; Rose et al.
  • Modeling Network Dynamics: the Lac Operon, a Case Study

    Modeling Network Dynamics: the Lac Operon, a Case Study

    JCBMini-Review Modeling network dynamics: the lac operon, a case study José M.G. Vilar,1 Ca˘ lin C. Guet,1,2 and Stanislas Leibler1 1The Rockefeller University, New York, NY 10021 2Department of Molecular Biology, Princeton University, Princeton, NJ 08544 We use the lac operon in Escherichia coli as a prototype components to entire cells. In contrast to what this wide- system to illustrate the current state, applicability, and spread use might indicate, such modeling has many limitations. limitations of modeling the dynamics of cellular networks. On the one hand, the cell is not a well-stirred reactor. It is a We integrate three different levels of description (molecular, highly heterogeneous and compartmentalized structure, in cellular, and that of cell population) into a single model, which phenomena like molecular crowding or channeling which seems to capture many experimental aspects of the are present (Ellis, 2001), and in which the discrete nature of system. the molecular components cannot be neglected (Kuthan, Downloaded from 2001). On the other hand, so few details about the actual in vivo processes are known that it is very difficult to proceed Modeling has had a long tradition, and a remarkable success, without numerous, and often arbitrary, assumptions about in disciplines such as engineering and physics. In biology, the nature of the nonlinearities and the values of the parameters however, the situation has been different. The enormous governing the reactions. Understanding these limitations, and www.jcb.org complexity of living systems and the lack of reliable quanti- ways to overcome them, will become increasingly impor- tative information have precluded a similar success.