CHAPTER 1 Introduction to Molecular Genetics and Genomics CHAPTER OUTLINE PRINCIPLES 1.1 DNA: The Genetic Material • Inherited traits are affected by genes. Experimental Proof of the Genetic Function of DNA • Genes are composed of the chemical deoxyribonucleic acid Genetic Role of DNA in (DNA). Bacteriophage • DNA replicates to form copies of itself that are identical 1.2 DNA Structure: The Double Helix (except for rare mutations). 1.3 An Overview of DNA Replication • DNA contains a genetic code specifying what types of enzymes and other proteins are made in cells. 1.4 Genes and Proteins Inborn Errors of Metabolism as a • DNA occasionally mutates, and the mutant forms specify Cause of Hereditary Disease altered proteins that have reduced activity or stability. Mutant Genes and Defective Proteins • A mutant enzyme is an “inborn error of metabolism” that 1.5 Gene Expression: The Central Dogma blocks one step in a biochemical pathway for the metabolism Transcription of small molecules. Translation The Genetic Code • Traits are affected by environment as well as by genes. 1.6 Mutation • Organisms change genetically through generations in the Protein Folding and Stability process of biological evolution. 1.7 Genes and Environment 1.8 Evolution: From Genes to Genomes, from Proteins to Proteomes The Molecular Unity of Life CONNECTIONS Natural Selection and Diversity Shear Madness Alfred D. Hershey and Martha Chase 1952 Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage The Black Urine Disease Archibald E. Garrod 1908 Inborn Errors of Metabolism 1 ach species of living organism has a terms of the abstract rules by which heredi- unique set of inherited characteristics tary elements (he called them “factors”) are that makes it different from other transmitted from parents to offspring. His Especies. Each species has its own develop- objects of study were garden peas, with mental plan—often described as a sort of variable traits like pea color and plant “blueprint” for building the organism— height. At one time genetics could be stud- which is encoded in the DNA molecules pre- ied only through the progeny produced sent in its cells. This developmental plan from matings. Genetic differences between determines the characteristics that are in- species were impossible to define, because herited. Because organisms in the same organisms of different species usually do not species share the same developmental plan, mate, or they produce hybrid progeny that organisms that are members of the same die or are sterile. This approach to the study species usually resemble one another, al- of genetics is often referred to as classical ge- though some notable exceptions usually are netics, or organismic or morphological ge- differences between males and females. For netics. Given the advances of molecular, or example, it is easy to distinguish a human modern, genetics, it is possible to study dif- being from a chimpanzee or a gorilla. A hu- ferences between species through the com- man being habitually stands upright and has parison and analysis of the DNA itself. There long legs, relatively little body hair, a large is no fundamental distinction between clas- brain, and a flat face with a prominent nose, sical and molecular genetics. They are dif- jutting chin, distinct lips, and small teeth. ferent and complementary ways of studying All of these traits are inherited—part of our the same thing: the function of the genetic developmental plan—and help set us apart material. In this book we include many ex- as Homo sapiens. amples showing how molecular and classi- But human beings are by no means cal genetics can be used in combination to identical. Many traits, or observable charac- enhance the power of genetic analysis. teristics, differ from one person to another. The foundation of genetics as a molecu- There is a great deal of variation in hair lar science dates back to 1869, just three color, eye color, skin color, height, weight, years after Mendel reported his exper- personality traits, and other characteristics. iments. It was in 1869 that Friedrich Some human traits are transmitted biologi- Miescher discovered a new type of weak cally, others culturally. The color of our acid, abundant in the nuclei of white blood eyes results from biological inheritance, but cells. Miescher’s weak acid turned out to be the native language we learned as a child the chemical substance we now call DNA results from cultural inheritance. Many (deoxyribonucleic acid). For many years traits are influenced jointly by biological in- the biological function of DNA was un- heritance and environmental factors. For known, and no role in heredity was as- example, weight is determined in part by cribed to it. This first section shows how inheritance but also in part by environ- DNA was eventually isolated and identified ment: how much food we eat, its nutri- as the material that genes are made of. tional content, our exercise regimen, and so forth. Genetics is the study of biologically inherited traits, including traits that are in- 1.1 fluenced in part by the environment. DNA: The Genetic Material The fundamental concept of genetics is That the cell nucleus plays a key role in in- that: heritance was recognized in the 1870s by the observation that the nuclei of male and Inherited traits are determined by the ele- female reproductive cells undergo fusion in ments of heredity that are transmitted from the process of fertilization. Soon thereafter, parents to offspring in reproduction; these elements of heredity are called genes. chromosomes were first observed inside the nucleus as thread-like objects that The existence of genes and the rules become visible in the light microscope governing their transmission from gen- when the cell is stained with certain dyes. eration to generation were first articulated Chromosomes were found to exhibit a by Gregor Mendel in 1866 (Chapter 3). characteristic “splitting” behavior in which Mendel’s formulation of inheritance was in each daughter cell formed by cell division 2 Chapter 1 Introduction to Molecular Genetics and Genomics receives an identical complement of chro- as the genetic material, and DNA was as- mosomes (Chapter 4). Further evidence for sumed to function merely as the structural the importance of chromosomes was pro- framework of the chromosomes. The ex- vided by the observation that, whereas the periments described below finally demon- number of chromosomes in each cell may strated that DNA is the genetic material. differ among biological species, the number of chromosomes is nearly always constant within the cells of any particular species. Experimental Proof of the Genetic These features of chromosomes were well Function of DNA understood by about 1900, and they made An important first step was taken by it seem likely that chromosomes were the Frederick Griffith in 1928 when he demon- carriers of the genes. strated that a physical trait can be passed By the 1920s, several lines of indirect from one cell to another. He was working evidence began to suggest a close relation- with two strains of the bacterium ship between chromosomes and DNA. Streptococcus pneumoniae identified as S and Microscopic studies with special stains R. When a bacterial cell is grown on solid showed that DNA is present in chromo- medium, it undergoes repeated cell divi- somes. Chromosomes also contain various sions to form a visible clump of cells called a types of proteins, but the amount and kinds colony. The S type of S. pneumoniae synthe- of chromosomal proteins differ greatly from sizes a gelatinous capsule composed of one cell type to another, whereas the complex carbohydrate (polysaccharide). amount of DNA per cell is constant. The enveloping capsule makes each colony Furthermore, nearly all of the DNA present large and gives it a glistening or smooth (S) in cells of higher organisms is present in the appearance. This capsule also enables the chromosomes. These arguments for DNA as bacterium to cause pneumonia by protect- the genetic material were unconvincing, ing it from the defense mechanisms of an however, because crude chemical analyses infected animal. The R strains of S. pneumo- had suggested (erroneously, as it turned niae are unable to synthesize the capsular out) that DNA lacks the chemical diversity polysaccharide; they form small colonies needed in a genetic substance. The favored that have a rough (R) surface (Figure 1.1). candidate for the genetic material was pro- This strain of the bacterium does not cause tein, because proteins were known to be an pneumonia, because without the capsule exceedingly diverse collection of molecules. the bacteria are inactivated by the immune Proteins therefore became widely accepted system of the host. Both types of bacteria FPO R strain S strain Figure 1.1 Colonies of rough (R, the small colonies) and smooth (S, the large colonies) strains of Streptococcus pneumoniae. The S colonies are larger because of the gelatinous capsule on the S cells. [Photograph from O. T. Avery, C. M. MacLeod, and M. McCarty. Reproduced from the Journal of Experimental Medicine, 1944, vol. 79, p. 137 by copyright permission of The Rockefeller University Press.] 1.1 DNA: The Genetic Material 3 Living Living Heat-killed Living R cells plus S cells R cells S cells heat-killed S cells Mouse contracts Mouse remains Mouse remains Mouse contracts pneumonia healthy healthy pneumonia S colonies isolated R colonies isolated No colonies isolated R and S colonies isolated from tissue of dead mouse from tissue from tissue from tissue of dead mouse Figure 1.2 The Griffith's experiment demonstrating bacterial transformation. A mouse remains healthy if injected with either the nonvirulent R strain of S. pneumoniae or heat-killed cell fragments of the usually virulent S strain. R cells in the presence of heat-killed S cells are transformed into the virulent S strain, causing pneumonia in the mouse.