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Introduction Open Genetics - Fall 2014 September, 2014 Version The first edition of this book was produced in January, 2009 as instructional material for students in Biology 207 at the University of Alberta, and is released to the public for non-commercial use under the Creative Commons License (See below). Users are encouraged to make modifications and improvements to the book. All text in the original edition was written by Michael Deyholos, Ph.D. Chapter 9 and portions of Chapters 2 and 3 in this edition were written by Mike Harrington, Ph.D. Additional content and editing by John Locke, Ph.D. and Mark Wolansky, M.Sc. Photos and some diagrams were obtained from various, non-copyrighted sources, including Flickr, Wikipedia, Public Library of Science, and Wikimedia Commons. Photo attributions are listed in the legend with each image. This work is licensed under the Creative Commons Attribution-NoncommercialShare Alike 2.5 Canada License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/2.5/ca/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Under the terms of the license, you are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work Under the following conditions: Attribution. You must include the name of the original author in books or excerpts derived from this work. Non-commercial. You may not use this work for commercial purposes. Share Alike. If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar licence to this one. For any reuse or distribution, you must make clear to others the licence terms of this work. Any of the above conditions can be waived if you get permission from the copyright holder. The author's moral rights are retained in this licence. Page I -i Introduction IMAGE, PHOTO AND FIGURE LICENSE DETAILS: The source of each figure is given at the end of the legend and includes the following: CC: AD Creative Commons Attribution-No Derivative Works 2.0 Generic CC: AN Creative Commons Attribution-Noncommercial 2.0 Generic CC: AND Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 Generic CC: AS Creative Commons Attribution-Share Alike 2.0 Generic EDU Educational use explicitly allowed by author, who retains copyright GFDL Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License PD Public Domain because it was created by a US government agency or because the author has explicitly released it into the public domain. BIBLIOGRAPHY Alberts, B. et al. 2004. "Molecular Biology of the Cell, fourth edition". Garland Science, New York Felix Ratjen, Gerd Döring, Cystic fibrosis, The Lancet, Volume 361, Issue 9358, 22 February 2003, Pages 681-689 Francis, Richard C. “Epigenetics”. 2011, Norton, NewYork. Griffiths, A. J. F. et al. 2005. "Introduction to Genetic Analysis, eighth edition." W. H. Freeman and Company, New York King, R. C. and W. D. Stansfield. 1997. "A Dictionary of Genetics, fifth edition". Oxford University Press, Toronto Lap-Chee Tsui and Ruslan Dorfman The Cystic Fibrosis Gene: A Molecular Genetic Perspective Cold Spring Harb Perspect, February 2013;3 MendelWeb. R. B. Blumberg, {August 1, 2012}. World Wide Web URL: www.mendelweb.org/ Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), {August 1, 2012}. World Wide Web URL: http://omim.org/ Watson, J. D. et al. 2008. "Molecular Biology of the Gene, sixth edition" Pearson Education, Inc., San Franciso Your Genes, Your Health Dolan DNA Learning Center / Cold Spring Harbor Laboratory, {August 1, 2012}. World Wide Web URL: www.ygyh.org/ Page I -ii Introduction TABLE OF CONTENTS Chapter 1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Introduction and Overview Overview DNA is the genetic material The structure of DNA Genes are the basic units of inheritance The function of genes The nuclear genome Model organisms facilitate genetic advances Chapter 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 Chromosomes, Mitosis, & Meiosis DNA is packaged into Chromatin Mitosis Meiosis The cell cycle and changes in DNA content Karyotypes Describe Chromosome Number and Structure Polyploidy arises from changes in whole sets of chromosomes Endo-reduplication Gene Balance Organellar genomes Chapter 3 3.1 3.2 3.3 3.4 3.5 3.6 3.7 Genetic Analysis of Single Genes Mendel's first law Relationships between genes, genotypes, and phenotypes Biochemical basis of dominance Crossing techniques used in classical genetics Sex-linkage: an exception to Mendel's first law Phenotypes may not be as expected from the genotype Phenotypic ratios may not be as expected Chapter 4 Mutation and Variation 4.1 Mutation and polymorphism 4.2 Origins of mutations 4.3 Genetic screening for mutations: forward genetics 4.4 Types of mutations 4.5 Some mutations may not have detectible phenotypes 4.6 Complementation tests and allelism 4.7 Example of human mutations Chapter 5 5.1 5.2 5.3 5.4 5.5 Pedigrees and Populations Pedigree analysis Inferring the mode of inheritance Sporadic and non-heritable diseases Calculating probabilities Population genetics Chapter 6 6.1 6.2 6.3 Genetic Analysis of Multiple Genes Dihybrid crosses Epistasis and other gene interactions Examples of multiple genes affecting one character Page I -iii Introduction Page I -iv Chapter 7 7.1 7.2 7.3 7.4 7.5 7.6 7.7 Linkage & Mapping Linkage Recombination Linkage reduces recombination frequency Crossovers allow recombination of linked loci Inferring recombination from genetic data Genetic mapping Mapping with three-point crosses Chapter 8 8.1 8.2 8.3 8.4 8.5 8.6 8.7 Techniques of Molecular Biology Isolating genomic DNA Isolating or detecting a specific sequence by PCR Cutting and pasting DNA: restriction digests and DNA ligation Cloning DNA: plasmid vectors DNA analysis: gel electrophoresis DNA analysis: blotting and hybridization Transgenic organisms Chapter 9 9.1 9.2 9.3 9.4 Changes in Chromosome Number & Structure Changes in chromosome number Changes in chromosome structure Chromosome abnormalities in humans Diagnosing human chromosome abnormalities Chapter 10 10.1 10.2 10.3 10.4 10.5 Molecular Markers & Quantitative Traits Some variations in the genome affect complex traits Origins of molecular polymorphisms Classification and detection of molecular markers Applications of molecular markers Quantitative trait locus (QTL) analysis Chapter 11 11.1 11.2 11.3 11.4 Genomics and Systems Biology 'Omics technologies DNA sequencing Whole genome sequencing Functional genomics – determining functions(s) Chapter 12 12.1 12.2 12.3 12.4 12.5 12.6 Regulation of Gene Expression The lac operon The use of mutants to study the lac operon Eukaryotic gene regulation Regulatory elements in evolution Additional levels of regulating transcription Epigentics Chapter 13 13.1 13.2 13.3 13.4 13.5 13.6 13.7 Cancer Genetics Classification of cancers Cancer cell biology Hallmarks of cancer Mutagens and carcinogens Oncogenes Tumor suppressor genes The “poster boy” of genetic research – Gleevec™