Bi 1x Spring 2014: LacI Titration
|
|
- Joy Hodge
- 5 years ago
- Views:
Transcription
1 Bi 1x Spring 2014: LacI Titration 1 Overview In this experiment, you will measure the effect of various mutated LacI repressor ribosome binding sites in an E. coli cell by measuring the expression of a yellow fluorescent protein. Using your skills of high-magnification phase and fluorescent microscopy coupled with some image processing tools, you will be able to measure the average protein copy number per cell! 2 Background In this section, we will cover the basics of gene regulation as well as a more detailed explanation of our experimental system. 2.1 Genetic Regulation What makes a human eye cell different from a skin cell? Both have the same set of genes, but clearly, they differ substantially in both structure and function. The reason, in part, is that although both cells share the same genes, they have different profiles of gene expression. If you think back to our lecture of genetics, we talked much about how genes are inherited across the biological scales and how we can identify the genotype of an organism by making observations of its phenotype, but we did not discuss in much detail how the genes were translated into an observable phenotype. The question of how gene expression is regulated is a major area of inquiry in contepmorary biology, both because of its importance to biological function, and because of the richness and diversity of gene regulation strategies that can be found in nature. Gene regulation occurs at all steps along the central dogma, from methylation of genomic DNA (known as epigenetics) to the chemical modifications made to proteins after translation that modulate its function or localization. In this final module, we will explore regulation of transcription using the LacI repressor molecule. Transcriptional regulation in prokaryotes is largely mediated by proteins that bind to DNA, called transcription factors (TFs). Most TFs bind specifically to a particluar DNA sequence known as an operator. For instance, the lac repressor protein binds srongly to the sequence AATTGTGAGCGCTCACAATT (refered to as O id ). TFs can be broadly categorized as either activators or repressors. Activators, as you can imagine, activate gene transcription by exhibiting favorable energetic interactions with the transcription machinery, such as RNA polymerase (). When an actiavor is bound near an binding site (known as a promoter ), it increases the rate of transcription by recruiting to its binding site. Repressors are proteins which inhibit gene transcription, usually by making the binding site less accessible. Many genes exhibit multiple TF binding sites surrounding the promoter region can quickly become quite complex, leading to exquisite control of when the gene is expressed. Often, the timing and abundnace of a protein can mean life or death for the cell. 2.2 The Lac Operon As we discussed in our lecture on genetics, the Lac operon is the canonical example of genetic regulation at the transcriptional level. In the perfect world of an E. coli cell, glucose is plentiful, antibiotic is absent, and there are no pesky Bi 1x students around to squish them onto agar pads 1
2 and blast them with high-intensity light. One can imagine that if glucose is present, there is no need to waste energy into building the machinery required to digest other carbon sources, such as lactose. However, if there is no glucose present yet lactose is plentiful, it would be in the organisms best interest to turn on expression of genes to help metabolize lactose. The Lac operon is sensitive to both concentration of glucose and lactose and initiates expression of the lactose metabolism genes (LacZ, LacY, and LacA) in the appropriate conditions. The general architecture of the lac operon is shown in Fig. 1. Lactose Absent No transcription LacI Promoter Operator LacZ, LacY, LacA Lactose Present Active transcription LacI mrna Promoter Operator LacZ, LacY, LacA Figure 1: The Lac operon. In absence of lactose, the repressor molecule LacI is bound to the operator, preventing transcription. In the presence of lactose, LacI is released from the DNA and transcription can proceed. The level of repression of the Lac operon is dependent on the number of LacI molecules present. If, for example, LacI were deleted from an E. coli cell, the LacZYA genes would be constitutively expressed. In our experiment, we will not measure the amount of LacZYA produced, but rather the abundance of yellow fluorescent protein (YFP). Prior to the lab, we have inserted a gene encoding YFP with the Lac operator O 2 (Fig. 2. Figure 2: Our experimental system. The YFP gene with the Lac repression promoter architecture has been inserted into the chromosome of E. coli (indicated by the elipses). In our system, we will not be directly measuring the presence of LacI. Rather, we will be measuring its effect on YFP expression. Intuitively, one would expect that the higher the concentration of LacI in the cell, the lower the level of gene expression one would obesreve. We can codify this intuition 2
3 mathematical by defining a quantity called the repression, where Repression = = Gene expression in the absence of repressor Gene expression in the presence of repressor YFP fluorescence in the absence of repressor YFP fluorescence in the presence of repressor (1) In other words, the repression tells us how many times less (or fold change ) a gene is expressed with LacI present than it would be if LacI were not present. Using the tools of statistical physics as discussed in lecture prior to the lab, we can take the next step and compute how this quantity depends on the physical parameters of our system: Repression = 1 + R N NS e ɛ rd/k B T, (2) where R is the number of repressor molecules, N NS is the number of nonspecific binding sites for the LacI repressor, ɛ rd is the energetic differece between the bound and unbound states of the LacI repressor, and k B T is the thermal energy. When testing a theoretical model, it is useful to have an experiment that allows you to independently tune the parameters of your model. In this experiment, you will test this model by tuning R. You will do this by using a set of E. coli strains that have been genetically engineered to express varying amounts of LacI. However, we won t tell you in advance what LacI copy number is for each strain; instead, you will use equation 3 to compute R for each of your experimental strains as part of your assignment. 3 Protocol Your kind and skilled TAs have prepared your samples ahead of time. Each group will be given a glass bottom dish with five E. coli-containing agarose pads. The pads will be laid out as follows: Figure 3: Agarose pad arrangement prepared before class The identity of each pad is as follows: 3
4 HG104::NoFluo - This strain has wild type levels of LacI, but does not have the YFP reporter. Therefore, it will only display autofluorescence. HG105::O2 - This strain produces no laci and will become the numerator of your repression measurement (see equation 1). Mystery strain I Mystery strain II Mystery strain III For each pad, you should take images at four to five different positions each containing five to ten cells for each field of view. Since you will be segmenting your images, be weary of cellular clumps in your field of view. Large numbers of clumped-together cells will make segmentation difficult if not impossible.. At each position you should take a phase contrast image as well as a FITC fluorescene image. Since you will be comparing different images, it is absolutely essential that each image is taken with the same exposure setting. To determine the appropriate exposure time, pick a field of cells on the HG105::O2 pad and test a range of exposure time ranging from 100 ms to several seconds. Do not use this position in your data set (why?). An appropriate exposure time will use 1/2 to 2/3 of the dynamic range of your camera (indicated by the curves in your settings window in Micro-Manager). Use the Multi-D acquisition window to take each image individually and save them in the appropriate folder. Your data sets will be uploaded the the course website. 4 Assignment Problem 0 (Summary). Write a brief summary of the experimental objectives, observations, and conclusions between one paragraph and one page in length. Problem 1 (Modalities of gene expression). From your understanding of gene expression, speculate on when we might expect a gene to only be activated? How about to only be repressed? Can you think of any case in which it would be advantageous for a gene to have little to no regulation? There is no right or wrong answer to this question. It is meant to get you thinking about regulation of gene expression as it relates to an organism s activities and struggles. Problem 2 (Example of your image overlay). For a phase fluorescent image of your choice, please show the following: 1. The original phase image. 2. The mask generated by your segmentation procedure. 3. An overlay of the original phase image and your final segementation mask. 4. An overlay of your final segmentation mask and the fluorescence image (in color). Be sure to include which pad your image came from as well as the code used for the processing. If 4
5 you do not have access to a color printer, print your color image in black and white, and Griffin your color image. Problem 3 (Calculating the number of LacI repressors per cell.). a) Using the HG104::NoFluo strain (Pad 1), compute and report the mean autofluorescence pixel value. b) For each of the other four strains, calculate the autofluorescence-corrected integrated fluorescence intensity of each detected cell. c) For each of the three experimental strains, compute the repression as defined by equation (1). I.e., compute Repression = = Gene expression in the absence of repressor Gene expression in the presence of repressor YFP fluorescence in the absence of repressor YFP fluorescence in the presence of repressor. (3) Here, the notation x refers to the value of x averaged over your samples. d) In lecture, we covered the basis of the statistical mechanical expression for repression defined by Repression = 1 + R N NS e ɛ rd/k B T, in which N NS is the number of possible nonspecific binding sites for LacI is is approximated by the length of the E. coli genome, base pairs. Why is this a good estimate? ɛ rd is the energetic difference of LacI bound to the operator versus unbound and is approximately 14.3k B T (Garcia and Phillips, PNAS, 2011). Calculate the number of repressors per cell, R, for each strain. Problem 4 (Cell-to-cell variability in gene expression). As you probably noticed while taking your images, not all E. coli cells on the same pad exhibit the same level of fluorescence (hence the average pixel intensities). This cell-to-cell variability in gene expression is known as the noise or variability in expression. A common measure of noise is the variance in gene expression normalized by the mean, or Fano factor. Mathematically, this translates to variance(gene Expression) Fano factor = mean(gene Expression) Compute the noise strength for each of your three experimental strains as well as for HG105. Make a scatter plot fo noise strength versus mean gene expression for each data point. Does the noise strength increase or decrease with increased gene expression? Problem 5 (Data and code). Attach all code, data, and sample images not specifically asked for in the other problems. 5
Chapter 15 Active Reading Guide Regulation of Gene Expression
Name: AP Biology Mr. Croft Chapter 15 Active Reading Guide Regulation of Gene Expression The overview for Chapter 15 introduces the idea that while all cells of an organism have all genes in the genome,
More informationCHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON
PROKARYOTE GENES: E. COLI LAC OPERON CHAPTER 13 CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON Figure 1. Electron micrograph of growing E. coli. Some show the constriction at the location where daughter
More informationREVIEW SESSION. Wednesday, September 15 5:30 PM SHANTZ 242 E
REVIEW SESSION Wednesday, September 15 5:30 PM SHANTZ 242 E Gene Regulation Gene Regulation Gene expression can be turned on, turned off, turned up or turned down! For example, as test time approaches,
More informationIntroduction. Gene expression is the combined process of :
1 To know and explain: Regulation of Bacterial Gene Expression Constitutive ( house keeping) vs. Controllable genes OPERON structure and its role in gene regulation Regulation of Eukaryotic Gene Expression
More informationthe noisy gene Biology of the Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB)
Biology of the the noisy gene Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB) day III: noisy bacteria - Regulation of noise (B. subtilis) - Intrinsic/Extrinsic
More informationName: SBI 4U. Gene Expression Quiz. Overall Expectation:
Gene Expression Quiz Overall Expectation: - Demonstrate an understanding of concepts related to molecular genetics, and how genetic modification is applied in industry and agriculture Specific Expectation(s):
More informationRegulation of Gene Expression
Chapter 18 Regulation of Gene Expression Edited by Shawn Lester PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley
More information3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization.
3.B.1 Gene Regulation Gene regulation results in differential gene expression, leading to cell specialization. We will focus on gene regulation in prokaryotes first. Gene regulation accounts for some of
More informationAP Bio Module 16: Bacterial Genetics and Operons, Student Learning Guide
Name: Period: Date: AP Bio Module 6: Bacterial Genetics and Operons, Student Learning Guide Getting started. Work in pairs (share a computer). Make sure that you log in for the first quiz so that you get
More informationLecture 18 June 2 nd, Gene Expression Regulation Mutations
Lecture 18 June 2 nd, 2016 Gene Expression Regulation Mutations From Gene to Protein Central Dogma Replication DNA RNA PROTEIN Transcription Translation RNA Viruses: genome is RNA Reverse Transcriptase
More informationControl of Gene Expression in Prokaryotes
Why? Control of Expression in Prokaryotes How do prokaryotes use operons to control gene expression? Houses usually have a light source in every room, but it would be a waste of energy to leave every light
More informationGene Switches Teacher Information
STO-143 Gene Switches Teacher Information Summary Kit contains How do bacteria turn on and turn off genes? Students model the action of the lac operon that regulates the expression of genes essential for
More informationComplete all warm up questions Focus on operon functioning we will be creating operon models on Monday
Complete all warm up questions Focus on operon functioning we will be creating operon models on Monday 1. What is the Central Dogma? 2. How does prokaryotic DNA compare to eukaryotic DNA? 3. How is DNA
More informationProkaryotic Gene Expression (Learning Objectives)
Prokaryotic Gene Expression (Learning Objectives) 1. Learn how bacteria respond to changes of metabolites in their environment: short-term and longer-term. 2. Compare and contrast transcriptional control
More informationGENE REGULATION AND PROBLEMS OF DEVELOPMENT
GENE REGULATION AND PROBLEMS OF DEVELOPMENT By Surinder Kaur DIET Ropar Surinder_1998@ yahoo.in Mob No 9988530775 GENE REGULATION Gene is a segment of DNA that codes for a unit of function (polypeptide,
More informationControl of Gene Expression
Control of Gene Expression Mechanisms of Gene Control Gene Control in Eukaryotes Master Genes Gene Control In Prokaryotes Epigenetics Gene Expression The overall process by which information flows from
More informationWelcome to Class 21!
Welcome to Class 21! Introductory Biochemistry! Lecture 21: Outline and Objectives l Regulation of Gene Expression in Prokaryotes! l transcriptional regulation! l principles! l lac operon! l trp attenuation!
More informationControlling Gene Expression
Controlling Gene Expression Control Mechanisms Gene regulation involves turning on or off specific genes as required by the cell Determine when to make more proteins and when to stop making more Housekeeping
More informationChapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes
Chapter 16 Lecture Concepts Of Genetics Tenth Edition Regulation of Gene Expression in Prokaryotes Chapter Contents 16.1 Prokaryotes Regulate Gene Expression in Response to Environmental Conditions 16.2
More informationREGULATION OF GENE EXPRESSION. Bacterial Genetics Lac and Trp Operon
REGULATION OF GENE EXPRESSION Bacterial Genetics Lac and Trp Operon Levels of Metabolic Control The amount of cellular products can be controlled by regulating: Enzyme activity: alters protein function
More informationRegulation of Gene Expression
Chapter 18 Regulation of Gene Expression PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationUNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11
UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11 REVIEW: Signals that Start and Stop Transcription and Translation BUT, HOW DO CELLS CONTROL WHICH GENES ARE EXPRESSED AND WHEN? First of
More informationBig Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Tuesday, December 27, 16
Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Enduring understanding 3.B: Expression of genetic information involves cellular and molecular
More informationTHE EDIBLE OPERON David O. Freier Lynchburg College [BIOL 220W Cellular Diversity]
THE EDIBLE OPERON David O. Freier Lynchburg College [BIOL 220W Cellular Diversity] You have the following resources available to you: Short bread cookies = DNA / genetic elements Fudge Mint cookies = RNA
More informationWarm-Up. Explain how a secondary messenger is activated, and how this affects gene expression. (LO 3.22)
Warm-Up Explain how a secondary messenger is activated, and how this affects gene expression. (LO 3.22) Yesterday s Picture The first cell on Earth (approx. 3.5 billion years ago) was simple and prokaryotic,
More informationAPGRU6L2. Control of Prokaryotic (Bacterial) Genes
APGRU6L2 Control of Prokaryotic (Bacterial) Genes 2007-2008 Bacterial metabolism Bacteria need to respond quickly to changes in their environment STOP u if they have enough of a product, need to stop production
More informationName Period The Control of Gene Expression in Prokaryotes Notes
Bacterial DNA contains genes that encode for many different proteins (enzymes) so that many processes have the ability to occur -not all processes are carried out at any one time -what allows expression
More informationCHAPTER : Prokaryotic Genetics
CHAPTER 13.3 13.5: Prokaryotic Genetics 1. Most bacteria are not pathogenic. Identify several important roles they play in the ecosystem and human culture. 2. How do variations arise in bacteria considering
More informationChapter 18: Control of Gene Expression
Chapter 18: Control of Gene Expression 海洋生物研究所 曾令銘 海事大樓 426 室分機 : 5326 Differential Expression of Genes Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions
More informationHonors Biology Reading Guide Chapter 11
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
More informationGene regulation I Biochemistry 302. Bob Kelm February 25, 2005
Gene regulation I Biochemistry 302 Bob Kelm February 25, 2005 Principles of gene regulation (cellular versus molecular level) Extracellular signals Chemical (e.g. hormones, growth factors) Environmental
More informationInitiation of translation in eukaryotic cells:connecting the head and tail
Initiation of translation in eukaryotic cells:connecting the head and tail GCCRCCAUGG 1: Multiple initiation factors with distinct biochemical roles (linking, tethering, recruiting, and scanning) 2: 5
More information32 Gene regulation, continued Lecture Outline 11/21/05
32 Gene regulation, continued Lecture Outline 11/21/05 Review the operon concept Repressible operons (e.g. trp) Inducible operons (e.g. lac) Positive regulation of lac () Practice applying the operon concept
More informationTopic 4 - #14 The Lactose Operon
Topic 4 - #14 The Lactose Operon The Lactose Operon The lactose operon is an operon which is responsible for the transport and metabolism of the sugar lactose in E. coli. - Lactose is one of many organic
More informationBME 5742 Biosystems Modeling and Control
BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various
More information56:198:582 Biological Networks Lecture 8
56:198:582 Biological Networks Lecture 8 Course organization Two complementary approaches to modeling and understanding biological networks Constraint-based modeling (Palsson) System-wide Metabolism Steady-state
More information16 CONTROL OF GENE EXPRESSION
16 CONTROL OF GENE EXPRESSION Chapter Outline 16.1 REGULATION OF GENE EXPRESSION IN PROKARYOTES The operon is the unit of transcription in prokaryotes The lac operon for lactose metabolism is transcribed
More informationDevelopment Team. Regulation of gene expression in Prokaryotes: Lac Operon. Molecular Cell Biology. Department of Zoology, University of Delhi
Paper Module : 15 : 23 Development Team Principal Investigator : Prof. Neeta Sehgal Department of Zoology, University of Delhi Co-Principal Investigator : Prof. D.K. Singh Department of Zoology, University
More informationUnit 3: Control and regulation Higher Biology
Unit 3: Control and regulation Higher Biology To study the roles that genes play in the control of growth and development of organisms To be able to Give some examples of features which are controlled
More informationControl of Prokaryotic (Bacterial) Gene Expression. AP Biology
Control of Prokaryotic (Bacterial) Gene Expression Figure 18.1 How can this fish s eyes see equally well in both air and water? Aka. Quatro ojas Regulation of Gene Expression: Prokaryotes and eukaryotes
More informationGene Regulation and Expression
THINK ABOUT IT Think of a library filled with how-to books. Would you ever need to use all of those books at the same time? Of course not. Now picture a tiny bacterium that contains more than 4000 genes.
More informationBacterial Genetics & Operons
Bacterial Genetics & Operons The Bacterial Genome Because bacteria have simple genomes, they are used most often in molecular genetics studies Most of what we know about bacterial genetics comes from the
More informationBoolean models of gene regulatory networks. Matthew Macauley Math 4500: Mathematical Modeling Clemson University Spring 2016
Boolean models of gene regulatory networks Matthew Macauley Math 4500: Mathematical Modeling Clemson University Spring 2016 Gene expression Gene expression is a process that takes gene info and creates
More informationNewly made RNA is called primary transcript and is modified in three ways before leaving the nucleus:
m Eukaryotic mrna processing Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: Cap structure a modified guanine base is added to the 5 end. Poly-A tail
More informationProkaryotic Gene Expression (Learning Objectives)
Prokaryotic Gene Expression (Learning Objectives) 1. Learn how bacteria respond to changes of metabolites in their environment: short-term and longer-term. 2. Compare and contrast transcriptional control
More informationVilla et al. (2005) Structural dynamics of the lac repressor-dna complex revealed by a multiscale simulation. PNAS 102:
Villa et al. (2005) Structural dynamics of the lac repressor-dna complex revealed by a multiscale simulation. PNAS 102: 6783-6788. Background: The lac operon is a cluster of genes in the E. coli genome
More informationLecture 4: Transcription networks basic concepts
Lecture 4: Transcription networks basic concepts - Activators and repressors - Input functions; Logic input functions; Multidimensional input functions - Dynamics and response time 2.1 Introduction The
More informationSlide 1 / 7. Free Response
Slide 1 / 7 Free Response Slide 2 / 7 Slide 3 / 7 1 The above diagrams illustrate the experiments carried out by Griffith and Hershey and Chaserespectively. Describe the hypothesis or conclusion that each
More informationPROTEIN SYNTHESIS INTRO
MR. POMERANTZ Page 1 of 6 Protein synthesis Intro. Use the text book to help properly answer the following questions 1. RNA differs from DNA in that RNA a. is single-stranded. c. contains the nitrogen
More informationProkaryotic Regulation
Prokaryotic Regulation Control of transcription initiation can be: Positive control increases transcription when activators bind DNA Negative control reduces transcription when repressors bind to DNA regulatory
More informationDNA Technology, Bacteria, Virus and Meiosis Test REVIEW
Be prepared to turn in a completed test review before your test. In addition to the questions below you should be able to make and analyze a plasmid map. Prokaryotic Gene Regulation 1. What is meant by
More information4. Why not make all enzymes all the time (even if not needed)? Enzyme synthesis uses a lot of energy.
1 C2005/F2401 '10-- Lecture 15 -- Last Edited: 11/02/10 01:58 PM Copyright 2010 Deborah Mowshowitz and Lawrence Chasin Department of Biological Sciences Columbia University New York, NY. Handouts: 15A
More informationBi 8 Lecture 11. Quantitative aspects of transcription factor binding and gene regulatory circuit design. Ellen Rothenberg 9 February 2016
Bi 8 Lecture 11 Quantitative aspects of transcription factor binding and gene regulatory circuit design Ellen Rothenberg 9 February 2016 Major take-home messages from λ phage system that apply to many
More informationThe Gene The gene; Genes Genes Allele;
Gene, genetic code and regulation of the gene expression, Regulating the Metabolism, The Lac- Operon system,catabolic repression, The Trp Operon system: regulating the biosynthesis of the tryptophan. Mitesh
More informationComputational Cell Biology Lecture 4
Computational Cell Biology Lecture 4 Case Study: Basic Modeling in Gene Expression Yang Cao Department of Computer Science DNA Structure and Base Pair Gene Expression Gene is just a small part of DNA.
More informationLesson Overview. Gene Regulation and Expression. Lesson Overview Gene Regulation and Expression
13.4 Gene Regulation and Expression THINK ABOUT IT Think of a library filled with how-to books. Would you ever need to use all of those books at the same time? Of course not. Now picture a tiny bacterium
More information1. In most cases, genes code for and it is that
Name Chapter 10 Reading Guide From DNA to Protein: Gene Expression Concept 10.1 Genetics Shows That Genes Code for Proteins 1. In most cases, genes code for and it is that determine. 2. Describe what Garrod
More informationRegulation of Gene Expression in Bacteria and Their Viruses
11 Regulation of Gene Expression in Bacteria and Their Viruses WORKING WITH THE FIGURES 1. Compare the structure of IPTG shown in Figure 11-7 with the structure of galactose shown in Figure 11-5. Why is
More informationSupplemental Materials
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION, May 2013, p. 107-109 DOI: http://dx.doi.org/10.1128/jmbe.v14i1.496 Supplemental Materials for Engaging Students in a Bioinformatics Activity to Introduce Gene
More information13.4 Gene Regulation and Expression
13.4 Gene Regulation and Expression Lesson Objectives Describe gene regulation in prokaryotes. Explain how most eukaryotic genes are regulated. Relate gene regulation to development in multicellular organisms.
More informationEukaryotic Gene Expression
Eukaryotic Gene Expression Lectures 22-23 Several Features Distinguish Eukaryotic Processes From Mechanisms in Bacteria 123 Eukaryotic Gene Expression Several Features Distinguish Eukaryotic Processes
More informationCo-ordination occurs in multiple layers Intracellular regulation: self-regulation Intercellular regulation: coordinated cell signalling e.g.
Gene Expression- Overview Differentiating cells Achieved through changes in gene expression All cells contain the same whole genome A typical differentiated cell only expresses ~50% of its total gene Overview
More informationRegulation of Gene Expression at the level of Transcription
Regulation of Gene Expression at the level of Transcription (examples are mostly bacterial) Diarmaid Hughes ICM/Microbiology VT2009 Regulation of Gene Expression at the level of Transcription (examples
More informationGLOBEX Bioinformatics (Summer 2015) Genetic networks and gene expression data
GLOBEX Bioinformatics (Summer 2015) Genetic networks and gene expression data 1 Gene Networks Definition: A gene network is a set of molecular components, such as genes and proteins, and interactions between
More informationRNA Synthesis and Processing
RNA Synthesis and Processing Introduction Regulation of gene expression allows cells to adapt to environmental changes and is responsible for the distinct activities of the differentiated cell types that
More informationRegulation of gene Expression in Prokaryotes & Eukaryotes
Regulation of gene Expression in Prokaryotes & Eukaryotes 1 The trp Operon Contains 5 genes coding for proteins (enzymes) required for the synthesis of the amino acid tryptophan. Also contains a promoter
More informationUNIT 5. Protein Synthesis 11/22/16
UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA
More informationMultiple Choice Review- Eukaryotic Gene Expression
Multiple Choice Review- Eukaryotic Gene Expression 1. Which of the following is the Central Dogma of cell biology? a. DNA Nucleic Acid Protein Amino Acid b. Prokaryote Bacteria - Eukaryote c. Atom Molecule
More informationBiology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall
Biology Biology 1 of 26 Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 2 of 26 Gene Regulation: An Example Gene Regulation: An Example
More informationThe Making of the Fittest: Evolving Switches, Evolving Bodies
INTRODUCTION MODELING THE REGULATORY SWITCHES OF THE PITX1 GENE IN STICKLEBACK FISH The types and amounts of proteins produced by a given cell in the body are very important and carefully regulated. Transcribing
More informationCS-E5880 Modeling biological networks Gene regulatory networks
CS-E5880 Modeling biological networks Gene regulatory networks Jukka Intosalmi (based on slides by Harri Lähdesmäki) Department of Computer Science Aalto University January 12, 2018 Outline Modeling gene
More informationRegulation of gene expression. Premedical - Biology
Regulation of gene expression Premedical - Biology Regulation of gene expression in prokaryotic cell Operon units system of negative feedback positive and negative regulation in eukaryotic cell - at any
More informationWeek 10! !
Week 10! 10-24-2013! Annotated Bibliography! Sources of papers! 3 papers! Peer-reviewed scientific literature (no review articles)! No more than 2 from:! the same author! the same journal! 2 of the 3 must
More informationComputational Biology: Basics & Interesting Problems
Computational Biology: Basics & Interesting Problems Summary Sources of information Biological concepts: structure & terminology Sequencing Gene finding Protein structure prediction Sources of information
More informationTranslation - Prokaryotes
1 Translation - Prokaryotes Shine-Dalgarno (SD) Sequence rrna 3 -GAUACCAUCCUCCUUA-5 mrna...ggagg..(5-7bp)...aug Influences: Secondary structure!! SD and AUG in unstructured region Start AUG 91% GUG 8 UUG
More informationTranslation and Operons
Translation and Operons You Should Be Able To 1. Describe the three stages translation. including the movement of trna molecules through the ribosome. 2. Compare and contrast the roles of three different
More informationGene regulation II Biochemistry 302. Bob Kelm February 28, 2005
Gene regulation II Biochemistry 302 Bob Kelm February 28, 2005 Catabolic operons: Regulation by multiple signals targeting different TFs Catabolite repression: Activity of lac operon is restricted when
More informationGENES AND CHROMOSOMES III. Lecture 5. Biology Department Concordia University. Dr. S. Azam BIOL 266/
GENES AND CHROMOSOMES III Lecture 5 BIOL 266/4 2014-15 Dr. S. Azam Biology Department Concordia University CELL NUCLEUS AND THE CONTROL OF GENE EXPRESSION OPERONS Introduction All cells in a multi-cellular
More information15.2 Prokaryotic Transcription *
OpenStax-CNX module: m52697 1 15.2 Prokaryotic Transcription * Shannon McDermott Based on Prokaryotic Transcription by OpenStax This work is produced by OpenStax-CNX and licensed under the Creative Commons
More informationLiving Mechanisms as Complex Systems
Living Mechanisms as Complex Systems The Traditional Mechanistic Perspective Decompose the organism into parts and operations Understand each on its own Link the whole together (sequentially, linearly)
More informationChapter 18 Regulation of Gene Expression
Chapter 18 Regulation of Gene Expression Differential gene expression Every somatic cell in an individual organism contains the same genetic information and replicated from the same original fertilized
More information2. Mathematical descriptions. (i) the master equation (ii) Langevin theory. 3. Single cell measurements
1. Why stochastic?. Mathematical descriptions (i) the master equation (ii) Langevin theory 3. Single cell measurements 4. Consequences Any chemical reaction is stochastic. k P d φ dp dt = k d P deterministic
More informationGene regulation II Biochemistry 302. February 27, 2006
Gene regulation II Biochemistry 302 February 27, 2006 Molecular basis of inhibition of RNAP by Lac repressor 35 promoter site 10 promoter site CRP/DNA complex 60 Lewis, M. et al. (1996) Science 271:1247
More informationBio 119 Bacterial Genomics 6/26/10
BACTERIAL GENOMICS Reading in BOM-12: Sec. 11.1 Genetic Map of the E. coli Chromosome p. 279 Sec. 13.2 Prokaryotic Genomes: Sizes and ORF Contents p. 344 Sec. 13.3 Prokaryotic Genomes: Bioinformatic Analysis
More information12-5 Gene Regulation
12-5 Gene Regulation Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 1 of 26 12-5 Gene Regulation Gene Regulation: An Example Gene
More informationPrinciples of Genetics
Principles of Genetics Snustad, D ISBN-13: 9780470903599 Table of Contents C H A P T E R 1 The Science of Genetics 1 An Invitation 2 Three Great Milestones in Genetics 2 DNA as the Genetic Material 6 Genetics
More informationMultistability in the lactose utilization network of Escherichia coli
Multistability in the lactose utilization network of Escherichia coli Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J. Ruby Abrams Agenda Motivation Intro to multistability Purpose
More informationBasic Synthetic Biology circuits
Basic Synthetic Biology circuits Note: these practices were obtained from the Computer Modelling Practicals lecture by Vincent Rouilly and Geoff Baldwin at Imperial College s course of Introduction to
More informationCh. 18 Regula'on of Gene Expression BIOL 222
Ch. 18 Regula'on of Gene Expression BIOL 222 Overview: Conduc'ng the Gene'c Orchestra Prokaryotes and eukaryotes alter gene expression in response to their changing environment In mul@cellular eukaryotes
More informationL3.1: Circuits: Introduction to Transcription Networks. Cellular Design Principles Prof. Jenna Rickus
L3.1: Circuits: Introduction to Transcription Networks Cellular Design Principles Prof. Jenna Rickus In this lecture Cognitive problem of the Cell Introduce transcription networks Key processing network
More information(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid.
1. A change that makes a polypeptide defective has been discovered in its amino acid sequence. The normal and defective amino acid sequences are shown below. Researchers are attempting to reproduce the
More information+ regulation. ribosomes
central dogma + regulation rpl DNA tsx rrna trna mrna ribosomes tsl ribosomal proteins structural proteins transporters enzymes srna regulators RNAp DNAp tsx initiation control by transcription factors
More informationStochastic simulations
Stochastic simulations Application to molecular networks Literature overview Noise in genetic networks Origins How to measure and distinguish between the two types of noise (intrinsic vs extrinsic)? What
More informationDivision Ave. High School AP Biology
Control of Prokaryotic (Bacterial) Genes 20072008 Bacterial metabolism n Bacteria need to respond quickly to changes in their environment u if they have enough of a product, need to stop production n why?
More informationEvolution in Action: The Power of Mutation in E. coli
Evolution in Action: The Power of Mutation in E. coli by Merle K. Heidemann, College of Natural Science, Emeritus Peter J. T. White, Lyman Briggs College James J. Smith, Lyman Briggs College Michigan State
More informationBiological Pathways Representation by Petri Nets and extension
Biological Pathways Representation by and extensions December 6, 2006 Biological Pathways Representation by and extension 1 The cell Pathways 2 Definitions 3 4 Biological Pathways Representation by and
More informationDesigner Genes C Test
Northern Regional: January 19 th, 2019 Designer Genes C Test Name(s): Team Name: School Name: Team Number: Rank: Score: Directions: You will have 50 minutes to complete the test. You may not write on the
More informationTranslation. Genetic code
Translation Genetic code If genes are segments of DNA and if DNA is just a string of nucleotide pairs, then how does the sequence of nucleotide pairs dictate the sequence of amino acids in proteins? Simple
More informationSupplementary Materials for
www.sciencemag.org/content/346/6216/1533/suppl/dc1 Supplementary Materials for Promoter architecture dictates cell-to-cell variability in gene expression Daniel L. Jones, Robert C. Brewster, Rob Phillips*
More information2. What was the Avery-MacLeod-McCarty experiment and why was it significant? 3. What was the Hershey-Chase experiment and why was it significant?
Name Date Period AP Exam Review Part 6: Molecular Genetics I. DNA and RNA Basics A. History of finding out what DNA really is 1. What was Griffith s experiment and why was it significant? 1 2. What was
More information